[English] 日本語
Yorodumi
- PDB-9mrv: Crystal structures of a cyanobacterial DAP epimerase bound to D,L... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mrv
TitleCrystal structures of a cyanobacterial DAP epimerase bound to D,L-alpha-methyl DAP
ComponentsDiaminopimelate epimerase
KeywordsANTIBIOTIC / DAP epimerase / diaminopimelic acid / DapF / cofactor-independent / protein biochemistry / enzyme mechanism / inhibitor / lysine biosynthesis
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
Similarity search - Domain/homology
(2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID / Diaminopimelate epimerase
Similarity search - Component
Biological speciesAnabaena sp. YBS01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsChen, P. / Lamer, T. / Vederas, J.C. / Lemieux, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Crystal structures of a cyanobacterial DAP epimerase bound to diaminopimelic acid analogues
Authors: Lamer, T. / Chen, P. / Lemieux, M.J. / Vederas, J.C.
History
DepositionJan 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diaminopimelate epimerase
B: Diaminopimelate epimerase
C: Diaminopimelate epimerase
D: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,5318
Polymers124,7144
Non-polymers8174
Water30,3191683
1
A: Diaminopimelate epimerase
hetero molecules

C: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7654
Polymers62,3572
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2810 Å2
ΔGint-10 kcal/mol
Surface area21230 Å2
MethodPISA
2
B: Diaminopimelate epimerase
hetero molecules

D: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7654
Polymers62,3572
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
Buried area2820 Å2
ΔGint-10 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.496, 103.878, 103.865
Angle α, β, γ (deg.)61.01, 78.42, 78.62
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Diaminopimelate epimerase / DAP epimerase / PLP-independent amino acid racemase


Mass: 31178.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. YBS01 (bacteria) / Gene: dapF, EH233_12580 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5Q0GFR1, diaminopimelate epimerase
#2: Chemical
ChemComp-ZDR / (2R,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID


Mass: 204.224 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H16N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1683 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.15M DL-Malic acid, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.69→46.21 Å / Num. obs: 181623 / % possible obs: 95.69 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.048 / Net I/σ(I): 10.24
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.69-1.790.334188430.8380.4721
1.79-1.910.197179950.9330.2781
1.91-2.070.116163470.9730.1631
2.07-2.260.074150710.9870.1041
2.26-2.530.054131600.9920.0761
2.53-2.920.039113490.9960.0551
2.92-3.570.02394140.9980.0331
3.57-5.040.01768290.9990.0231
5.04-46.210.01735200.9990.0241

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→46.21 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 9058 4.99 %
Rwork0.2016 --
obs0.2017 181623 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8508 0 56 1683 10247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068740
X-RAY DIFFRACTIONf_angle_d0.98911880
X-RAY DIFFRACTIONf_dihedral_angle_d14.4023196
X-RAY DIFFRACTIONf_chiral_restr0.0551348
X-RAY DIFFRACTIONf_plane_restr0.011564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.710.36923160.35695363X-RAY DIFFRACTION89
1.71-1.730.28833040.29625571X-RAY DIFFRACTION93
1.73-1.750.30243060.29795617X-RAY DIFFRACTION93
1.75-1.770.2742750.28565619X-RAY DIFFRACTION94
1.77-1.790.29592640.27525612X-RAY DIFFRACTION94
1.79-1.820.30583070.27545738X-RAY DIFFRACTION94
1.82-1.840.26593110.26665603X-RAY DIFFRACTION94
1.84-1.870.23582960.2655612X-RAY DIFFRACTION94
1.87-1.90.2663290.25745746X-RAY DIFFRACTION95
1.9-1.930.25583350.24615584X-RAY DIFFRACTION94
1.93-1.960.2562980.23365734X-RAY DIFFRACTION95
1.96-20.24082840.23395748X-RAY DIFFRACTION95
2-2.040.25383130.23825711X-RAY DIFFRACTION95
2.04-2.080.26193090.235727X-RAY DIFFRACTION95
2.08-2.130.24132720.23725713X-RAY DIFFRACTION95
2.13-2.180.26592540.23555860X-RAY DIFFRACTION96
2.18-2.230.23052420.23435797X-RAY DIFFRACTION96
2.23-2.290.24912980.22985831X-RAY DIFFRACTION96
2.29-2.360.24893080.22635810X-RAY DIFFRACTION96
2.36-2.430.21732860.21735766X-RAY DIFFRACTION97
2.43-2.520.21883180.21885862X-RAY DIFFRACTION97
2.52-2.620.23793220.22475813X-RAY DIFFRACTION97
2.62-2.740.21082860.22785849X-RAY DIFFRACTION97
2.74-2.890.2323190.22325871X-RAY DIFFRACTION97
2.89-3.070.19643240.20255865X-RAY DIFFRACTION98
3.07-3.30.17863000.18325933X-RAY DIFFRACTION98
3.3-3.630.15852840.15685948X-RAY DIFFRACTION98
3.64-4.160.13973120.13955906X-RAY DIFFRACTION98
4.16-5.240.12493710.12035894X-RAY DIFFRACTION99
5.24-46.210.17893150.16655862X-RAY DIFFRACTION98

+
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