[English] 日本語
Yorodumi
- PDB-5m47: Crystal structure of DapF from Corynebacterium glutamicum in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m47
TitleCrystal structure of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
2,6-DIAMINOPIMELIC ACID / Diaminopimelate epimerase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.
Authors: Sagong, H.Y. / Kim, K.J.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 18, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2452
Polymers30,0551
Non-polymers1901
Water1,22568
1
A: Diaminopimelate epimerase
hetero molecules

A: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4904
Polymers60,1092
Non-polymers3802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_554-y+1/4,-x+1/4,-z-3/41
Unit cell
Length a, b, c (Å)155.695, 155.695, 155.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332

-
Components

#1: Protein Diaminopimelate epimerase / DAP epimerase


Mass: 30054.732 Da / Num. of mol.: 1 / Fragment: Epimerase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: dapF, Cgl1943, cg2129 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8NP73, diaminopimelate epimerase
#2: Chemical ChemComp-API / 2,6-DIAMINOPIMELIC ACID


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.3 Å3/Da / Density % sol: 76.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Sodium citrate, CHES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 15, 2015
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.59→110.1 Å / Num. obs: 19071 / % possible obs: 97.4 % / Redundancy: 12 % / Rmerge(I) obs: 0.115 / Rsym value: 0.344 / Net I/σ(I): 21.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data collection
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H2Y

5h2y


Resolution: 2.59→110.09 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.502 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 976 4.9 %RANDOM
Rwork0.1914 ---
obs0.1932 19071 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.57 Å2 / Biso mean: 34.446 Å2 / Biso min: 8.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.59→110.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 13 68 2154
Biso mean--30.76 27.82 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192122
X-RAY DIFFRACTIONr_bond_other_d0.0020.021989
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.9532887
X-RAY DIFFRACTIONr_angle_other_deg1.12234565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4785279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37424.46894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1615322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6971514
X-RAY DIFFRACTIONr_chiral_restr0.1160.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02470
X-RAY DIFFRACTIONr_mcbond_it2.713.2331119
X-RAY DIFFRACTIONr_mcbond_other2.5343.2311118
X-RAY DIFFRACTIONr_mcangle_it4.3874.8411397
LS refinement shellResolution: 2.594→2.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 65 -
Rwork0.368 1323 -
all-1388 -
obs--94.04 %

+
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