[English] 日本語
Yorodumi
- PDB-2kct: Solution nmr structure of the ob-fold domain of heme chaperone cc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kct
TitleSolution nmr structure of the ob-fold domain of heme chaperone ccme from desulfovibrio vulgaris. northeast structural genomics target dvr115g.
ComponentsCytochrome c-type biogenesis protein CcmE
KeywordsCHAPERONE / solution NMR structure / heme chaperone / cytochrome c biogenesis / OB-fold domain / NESG / PSI-2 / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


protein-heme linkage / cytochrome complex assembly / membrane => GO:0016020 / heme binding / plasma membrane
Similarity search - Function
CcmE/CycJ protein / CcmE-like superfamily / CcmE / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Cytochrome c-type biogenesis protein CcmE
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsAramini, J.M. / Rossi, P. / Lee, H. / Lemak, A. / Wang, H. / Foote, E.L. / Jiang, M. / Xiao, R. / Nair, R. / Swapna, G.V.T. ...Aramini, J.M. / Rossi, P. / Lee, H. / Lemak, A. / Wang, H. / Foote, E.L. / Jiang, M. / Xiao, R. / Nair, R. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution nmr structure of the ob-fold domain of heme chaperone ccme from desulfovibrio vulgaris. northeast structural genomics target dvr115g.
Authors: Aramini, J.M. / Rossi, P. / Lee, H. / Lemak, A. / Wang, H. / Foote, E.L. / Jiang, M. / Xiao, R. / Nair, R. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Everett, J.K. / Montelione, G.T.
History
DepositionDec 29, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: pdbx_nmr_sample_details / pdbx_nmr_software ...pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name ..._pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c-type biogenesis protein CcmE


Theoretical massNumber of molelcules
Total (without water)10,3761
Polymers10,3761
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1

-
Components

#1: Protein Cytochrome c-type biogenesis protein CcmE


Mass: 10375.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: ccmE, DVU_1051 / Plasmid: DvR115G-21.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q72D78

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D SIMULTANEOUS CN NOESY
1413D 1H-13C NOESY aromatic
1512D 1H-13C HSQC HIGH RES. (L/V METHYL STEREOASSIGNMENT)
1613D HNCO
1713D HN(CO)CA
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D HN(CA)CO
11213D C(CO)NH TOCSY
11313D (H)CCH-COSY ALIPHATIC
11413D (H)CCH- TOCSY ALIPHATIC
11513D (H)CCH- TOCSY ALIPHATIC
11613D HNHA
11712D 1H-15N HETNOE
11811D 1H-15N T1 AND T2
11932D 1H-15N TROSY (for N-H RDC's)
NMR detailsText: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/ PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C- TERMINAL HHHHHH): BACKBONE, 98.6%, SIDE CHAIN, 97.2%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 43 TO 130, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 52-67,70-79,86-112,115-127: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 0.9. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 93.9%, ADDITIONALLY ALLOWED, 6.1%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.62/-2.12, ALL, -0.43/-2.54. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 10.87/-0.34 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 43-130): RECALL, 0.984, PRECISION, 0.915, F-MEASURE, 0.948, DP-SCORE, 0.795. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 4. (G) AGREEMENT WITH RESIDUAL DIPOLAR COUPLINGS (20 MODELS): CORRELATION COEFFICIENT (R): 0.995 (0.001); Q RMS: 0.096 (0.011). THE C- TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 43-51,68-69, 80-85,113-114,128-130.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM [U-100% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.56 mM [U-5% 13C; U-100% 15N] DvR115G, 20 mM ammonium acetate, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
310 % [U-5% 13C; U-100% 15N] DvR115G, 4.2 % PEG/hexanol, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMDvR115G[U-100% 13C; U-100% 15N]1
20 mMammonium acetate1
200 mMsodium chloride1
5 mMcalcium chloride1
10 mMDTT1
0.02 %sodium azide1
50 uMDSS1
0.56 mMDvR115G[U-5% 13C; U-100% 15N]2
20 mMammonium acetate2
200 mMsodium chloride2
5 mMcalcium chloride2
10 mMDTT2
0.02 %sodium azide2
50 uMDSS2
10 %DvR115G[U-5% 13C; U-100% 15N]3
4.2 %PEG/hexanol3
Sample conditionsIonic strength: 0.2 / pH: 4.5 / Pressure: AMBIENT / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER, ADAMS, CLORE, GROS, NILGESrefinement
TopSpin2.1structure solution
VnmrJ2.1Bstructure solution
NMRPipe2.3structure solution
Sparky3.112structure solution
PINEstructure solution
AutoAssign2.4.0structure solution
CYANA3structure solution
AutoStructure2.2.1structure solution
PSVS1.3structure solution
PdbStat5.1structure solution
PALESstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1384 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 79 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (16.8 ...Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1384 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 79 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (16.8 CONSTRAINTS PER RESIDUE, 6.0 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 43 TO 130 BY PSVS 1.3). IN ADDITION, 49 RESOLVED N-H RESIDUAL DIPOLAR COUPLINGS FOR ORDERED RESIDUES WERE INCLUDED IN ALL STRUCTURE CALCULATIONS. STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19.
NMR constraintsNOE constraints total: 1384 / NOE intraresidue total count: 344 / NOE long range total count: 525 / NOE medium range total count: 125 / NOE sequential total count: 390 / Protein chi angle constraints total count: 2 / Protein other angle constraints total count: 2 / Protein phi angle constraints total count: 37 / Protein psi angle constraints total count: 38
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.01 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more