[English] 日本語
Yorodumi
- PDB-2otn: Crystal structure of the catalytically active form of diaminopime... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2otn
TitleCrystal structure of the catalytically active form of diaminopimelate epimerase from Bacillus anthracis
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / Bacillus anthracis diaminopimelate epimerase / DAP / lysine metabolism / lanthionine
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
Diaminopimelate epimerase
Similarity search - Component
Biological speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMatho, M.H. / Fukuda, K. / Santelli, E. / Jaroszewski, L. / Liddington, R.C. / Roper, D.
CitationJournal: To be Published
Title: Crystal structure and inhibition of a catalytically active form of diaminopimelate epimerase (DapF)from Bacillus anthracis
Authors: Matho, M.H. / Fukuda, K. / Lloyd, A.J. / Santelli, E. / Jaroszewski, L. / Scott, D.J. / Liddington, R.C. / Roper, D.
History
DepositionFeb 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diaminopimelate epimerase
B: Diaminopimelate epimerase


Theoretical massNumber of molelcules
Total (without water)67,6272
Polymers67,6272
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.863, 87.334, 110.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Diaminopimelate epimerase


Mass: 33813.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Ames / Gene: dapF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Rosetta) / References: UniProt: Q81XR2, diaminopimelate epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / pH: 6.6
Details: 0.2 M ammonium formate, 20% PEG 3350, 3% ethylene glycol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24966 / % possible obs: 98.9 % / Observed criterion σ(I): -4 / Redundancy: 6.7 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GQZ

1gqz


Resolution: 2.4→36.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 17.426 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1234 5 %RANDOM
Rwork0.18 ---
obs0.184 23674 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.879 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å20 Å2
2--0.51 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 0 240 4710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224553
X-RAY DIFFRACTIONr_bond_other_d0.0010.023034
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.966160
X-RAY DIFFRACTIONr_angle_other_deg1.14537427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7324.829205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21515783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4021524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02882
X-RAY DIFFRACTIONr_nbd_refined0.1820.2719
X-RAY DIFFRACTIONr_nbd_other0.1980.23102
X-RAY DIFFRACTIONr_nbtor_refined0.170.22098
X-RAY DIFFRACTIONr_nbtor_other0.0860.22638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.49723726
X-RAY DIFFRACTIONr_mcbond_other0.87421191
X-RAY DIFFRACTIONr_mcangle_it4.19334629
X-RAY DIFFRACTIONr_scbond_it5.46941924
X-RAY DIFFRACTIONr_scangle_it6.7551531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 83 -
Rwork0.275 1579 -
obs--91.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.84182.0978-0.25913.42580.41492.24150.0302-0.19780.17450.028-0.16520.2598-0.1306-0.29950.1349-0.27760.0346-0.0166-0.1633-0.0343-0.12-13.906-0.07222.413
21.95380.021.2452.54230.06885.36320.18990.1912-0.1705-0.2542-0.00490.19840.23820.0665-0.1851-0.17490.0046-0.056-0.1425-0.10530.1168-22.581-14.260.418
36.28240.918-0.05853.21470.30992.5421-0.0504-0.1990.2680.01280.1125-0.26950.05710.3887-0.0621-0.27960.0286-0.0032-0.155-0.0379-0.108913.694-4.01522.455
42.1628-0.4305-4.20781.99211.293712.39670.85030.51910.396-0.3211-0.0769-0.0417-1.4647-0.9725-0.77340.02030.11920.113-0.03070.03130.463721.64514.1870.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-4 - 12516 - 145
2X-RAY DIFFRACTION1AA277 - 287297 - 307
3X-RAY DIFFRACTION2AA126 - 276146 - 296
4X-RAY DIFFRACTION3BB-1 - 12519 - 145
5X-RAY DIFFRACTION3BB277 - 287297 - 307
6X-RAY DIFFRACTION4BB126 - 276146 - 296

+
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