BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB
Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement

Northeast Structural Genomics Consortium

Binchen Mao, Rongjin Guan, and Gaetano T. Montelione

Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, and Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ
Piscataway, New Jersey 08854, USA





Abstract: Molecular replacement (MR) is widely used for addressing the phase problem in X-ray crystallography. Historically, crystallographers have had limited success using NMR structures as MR search models. Here, we report a comprehensive investigation of the utility of protein NMR ensembles as MR search models, using data for 25 pairs of X-ray and NMR structures solved and refined using modern NMR methods. Starting from NMR ensembles prepared by an improved protocol, FindCore, correct MR solutions were obtained for 22 targets. Based on these solutions, automatic model rebuilding could be done successfully. Rosetta refinement of NMR structures provided MR solutions for another two proteins. We also demonstrate that such properly prepared NMR ensembles and X-ray crystal structures have similar performance when used as MR search models for homologous structures, particularly for targets with sequence identity >40%.

PMID:21645849 [PubMed - in process]

Structure. 2011 Jun 8;19(6):757-66.





Dataset for MR study
XRAY NMR
NESG_ID XRay_PDB_ID Sequence      Length      Resolution(Å) Space group Coordinates Structure factor NMR_PDB_ID Sequence Oligomer Coordinates Constraints BMRB ID Chemical Shift Peaks Listb FIDb       RDC      
BeR31 3CPK 3CPK.seq 1502.5P432123CPK.pdb 3CPK-sf.cif 2K2E 2K2E.seq monomer2K2E.pdb 2K2E.mr 15702 15702.bmrb NANAPhage
CcR55 2O0Q 2O0Q.seq 1151.8C2222O0Q.pdb 2O0Q-sf.cif 2JQN 2JQN.seq monomer2JQN.pdb 2JQN.mr 15281 15281.bmrb 15281.peaks15281.fid NA
CsR4 2OTA 2OTA.seq 76 (2)2.2P2121212OTA.pdb 2OTA-sf.cif 2JR2 2JR2.seq dimer2JR2.pdb 2JR2.mr 15317 15317.bmrb 15317.peaks 15317.fid PEG PEG+CTAB
CtR107 3E0H 3E0H.seq 1581.8P2121213E0H.pdb 3E0H-sf.cif 2KCU 2KCU.seq monomer2KCU.pdb 2KCU.mr 16097 16097.bmrb 16097.peaks16097.fidPEG Phage
CtR148A 3IBW 3IBW.seq 88 (2)1.9P432123IBW.pdb 3IBW-sf.cif 2KO1 2KO1.seq dimer2KO1.pdb 2KO1.mr 16486 16486.bmrb 16486.peaks 16486.fidPAG PEG
DrR147Da 3GGN 3GGN.seq 155 (2)2.0P12113GGN.pdb 3GGN-sf.cif 2KCZ 2KCZ.seq monomer2KCZ.pdb 2KCZ.mr 16100 16100.bmrb 16100.peaks16100.fidNA
GmR137 3CWI 3CWI.seq 781.9P432123CWI.pdb 3CWI-sf.cif 2K5P 2K5P.seq monomer2K5P.pdb 2K5P.mr 15844 15844.bmrb 15844.peaks15844.fid PEG Phage
HR1958 1TVG 1TVG.seq 1531.6C1211TVG.pdb 1TVG-sf.cif 1XPW 1XPW.seq monomer1XPW.pdb 1XPW.mr 6344 6344.bmrb 6344.peaks6344.fid NA
HR3646E 3FIA 3FIA.seq 1211.5C1213FIA.pdb 3FIA-sf.cif 2KHN 2KHN.seq monomer2KHN.pdb 2KHN.mr 16250 16250.bmrb 16250.peaks16250.fidPAG PEG
HR41 3EVX 3EVX.seq 175 (4)2.5P13EVX.pdb 3EVX-sf.cif 2K07 2K07.seq monomer2K07.pdb 2K07.mr 6546 6546.bmrb 6546.peaks6546.fid NA
MbR242E 3GW2 3GW2.seq 1082.1P64223GW2.pdb 3GW2-sf.cif 2KKO 2KKO.seq dimer2KKO.pdb 2KKO.mr 16368 16368.bmrb 16368.peaks 16368.fid PAG PEG
MrR110B 3E0E 3E0E.seq 971.6P2121213E0E.pdb 3E0E-sf.cif 2K5V 2K5V.seq monomer2K5V.pdb 2K5V.mr 15849 15849.bmrb 15849.peaks 15849.fid NA
OR8C 2RHK 2RHK.seq 140 (2), 72 (2)2.0P412RHK.pdb 2RHK-sf.cif 2KKZ 2KKZ.seq monomer2KKZ.pdb 2KKZ.mr 16376 16376.bmrb 16376.peaks 16376.fidNA
PfR193A 3IDU 3IDU.seq 127 (2)1.7P12113IDU.pdb 3IDU-sf.cif 2KL6 2KL6.seq monomer2KL6.pdb 2KL6.mr 16385 16385.bmrb 16385.peaks NAPhage
PsR293 3H9X 3H9X.seq 125 (4)2.5P13H9X.pdb 3H9X-sf.cif 2KFP 2KFP.seq monomer2KFP.pdb 2KFP.mr 16186 16186.bmrb 16186.peaks 16186.fid NA
SR213 2IM8 2IM8.seq 131 (2)2.0P2121212IM8.pdb 2IM8-sf.cif 2HFI 2HFI.seq monomer2HFI.pdb 2HFI.mr 16113 16113.bmrb NA16113.fid NA
SR384 3BHP 3BHP.seq 60 (3)2.0C1213BHP.pdb 3BHP-sf.cif 2JVD 2JVD.seq monomer2JVD.pdb 2JVD.mr 15476 15476.bmrb 15476.peaks 15476.fid NA
SR478 2GSV 2GSV.seq 80 (2)1.9P1212GSV.pdb 2GSV-sf.cif 2JS1 2JS1.seq dimer2JS1.pdb 2JS1.mr 15350 15350.bmrb 15350.peaks15350.fidNA
SgR42 3C4S 3C4S.seq 66 (2)1.7P323C4S.pdb 3C4S-sf.cif 2JZ2 2JZ2.seq monomer2JZ2.pdb 2JZ2.mr 15604 15604.bmrb 15604.peaks NAPEG
SoR77 2QTI 2QTI.seq 802.3P432122QTI.pdb 2QTI-sf.cif 2JUW 2JUW.seq dimer2JUW.pdb 2JUW.mr 15456 15456.bmrb 15456.peaks 15456.fid PAG
SsR10 2Q00 2Q00.seq 129 (2)2.4I41222Q00.pdb 2Q00-sf.cif 2JPU 2JPU.seq monomer2JPU.pdb 2JPU.mr 15265 15265.bmrb 15265.peaks 15265.fidNA
StR65 2ES9 2ES9.seq 1152.0I2132ES9.pdb 2ES9-sf.cif 2JN8 2JN8.seq monomer2JN8.pdb 2JN8.mr 15089 15089.bmrb 15089.peaksNANA
StR70 2ES7 2ES7.seq 142 (4)2.8P12112ES7.pdb 2ES7-sf.cif 2JZT 2JZT.seq monomer2JZT.pdb 2JZT.mr 7178 7178.bmrb NANANA
XcR50 1TTZ 1TTZ.seq 872.1P651TTZ.pdb 1TTZ-sf.cif 1XPV 1XPV.seq monomer1XPV.pdb 1XPV.mr 6363 6363.bmrb 6363.peaksNANA
ZR18 2FFM 2FFM.seq 912.5P412122FFM.pdb 2FFM-sf.cif 1PQX 1PQX.seq monomer1PQX.pdb 1PQX.mr 5844 5844.bmrb NA5844.fid NA
a: Part of the NMR structure is not well defined (residue 24-69 out of 155 residues).
b: 'Submit' means data has been sumbitted to BMRB but has not been updated thus far.