[English] 日本語
Yorodumi
- PDB-6wfh: Streptomyces coelicolor methylmalonyl-CoA epimerase substrate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wfh
TitleStreptomyces coelicolor methylmalonyl-CoA epimerase substrate complex
ComponentsMethylmalonyl-CoA epimerase
KeywordsISOMERASE / Epimerase / acid-base / enol / enolate
Function / homology
Function and homology information


methylmalonyl-CoA epimerase activity / L-methylmalonyl-CoA metabolic process / metal ion binding
Similarity search - Function
Methylmalonyl-CoA epimerase / : / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Chem-V0V / VOC domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsStunkard, L.M. / Benjamin, A.B. / Bower, J.B. / Huth, T.J. / Lohman, J.R.
CitationJournal: Chembiochem / Year: 2022
Title: Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase.
Authors: Stunkard, L.M. / Benjamin, A.B. / Bower, J.B. / Huth, T.J. / Lohman, J.R.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 26, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3307
Polymers16,0601
Non-polymers1,2706
Water2,072115
1
A: Methylmalonyl-CoA epimerase
hetero molecules

A: Methylmalonyl-CoA epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,66014
Polymers32,1202
Non-polymers2,54112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPISA
Unit cell
Length a, b, c (Å)68.302, 68.302, 103.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-391-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Methylmalonyl-CoA epimerase / Ethylmalonyl-CoA epimerase


Mass: 16059.767 Da / Num. of mol.: 1 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO5398 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L2C2

-
Non-polymers , 6 types, 121 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-V0V / (3S,5R,9R,19E)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,19-tetrahydroxy-8,8,20-trimethyl-10,14-dioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicos-19-en-21-oic acid 3,5-dioxide (non-preferred name)


Mass: 867.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25 mM sodium chloride, 100 mM Bis-Tris:HCl pH 7.0, 2.7 M ammonium sulfate, 5% PEG 400

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 23, 2020 / Details: MD2 Micro Diffractometer
Diffraction measurementDetails: 1.00 degrees, -1.0 sec, detector distance 199.45 mm
Method: \w scans
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionAv R equivalents: 0.12 / Number: 288418
ReflectionResolution: 1.84→30 Å / Num. obs: 21795 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.035 / Rrim(I) all: 0.126 / Rsym value: 0.12 / Χ2: 0.999 / Net I/av σ(I): 18.968 / Net I/σ(I): 9
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 2.632 / Num. unique obs: 2123 / Rsym value: 1.103 / % possible all: 100
Cell measurementReflection used: 288418

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
ARP/wARPmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JC5

1jc5


Resolution: 1.84→29.31 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.2153 / WRfactor Rwork: 0.1832 / FOM work R set: 0.8702 / SU B: 2.108 / SU ML: 0.062 / SU R Cruickshank DPI: 0.088 / SU Rfree: 0.0866 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 1029 4.7 %RANDOM
Rwork0.1643 ---
obs0.1653 20711 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.82 Å2 / Biso mean: 37.613 Å2 / Biso min: 26.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å2-0 Å2-0 Å2
2--0.92 Å2-0 Å2
3----1.84 Å2
Refinement stepCycle: final / Resolution: 1.84→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 73 118 1266
Biso mean--54.94 50.82 -
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131174
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171049
X-RAY DIFFRACTIONr_angle_refined_deg2.1331.7121593
X-RAY DIFFRACTIONr_angle_other_deg1.5571.6282422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4825140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10921.36466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57315181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7361510
X-RAY DIFFRACTIONr_chiral_restr0.270.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
LS refinement shellResolution: 1.842→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 70 -
Rwork0.232 1424 -
all-1494 -
obs--94.92 %

+
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