[English] 日本語
Yorodumi
- PDB-3wb9: Crystal Structures of meso-diaminopimelate dehydrogenase from Sym... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wb9
TitleCrystal Structures of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum
ComponentsDiaminopimelate dehydrogenase
KeywordsOXIDOREDUCTASE / domain motion / thermo-stable / d-amino acid dehydrogenase
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / nucleotide binding
Similarity search - Function
Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesSymbiobacterium thermophilum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsLiu, W.D. / Li, Z. / Huang, C.H. / Guo, R.T. / Wu, Q.Q. / Zhu, D.M.
CitationJournal: Chembiochem / Year: 2014
Title: Structural and mutational studies on the unusual substrate specificity of meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum.
Authors: Liu, W. / Li, Z. / Huang, C.H. / Guo, R.T. / Zhao, L. / Zhang, D. / Chen, X. / Wu, Q. / Zhu, D.
History
DepositionMay 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diaminopimelate dehydrogenase
B: Diaminopimelate dehydrogenase
C: Diaminopimelate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,85813
Polymers99,9373
Non-polymers92110
Water20,5911143
1
A: Diaminopimelate dehydrogenase
B: Diaminopimelate dehydrogenase
C: Diaminopimelate dehydrogenase
hetero molecules

A: Diaminopimelate dehydrogenase
B: Diaminopimelate dehydrogenase
C: Diaminopimelate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,71626
Polymers199,8746
Non-polymers1,84220
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area30680 Å2
ΔGint-162 kcal/mol
Surface area65370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.249, 99.450, 80.822
Angle α, β, γ (deg.)90.000, 107.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-578-

HOH

21C-816-

HOH

-
Components

#1: Protein Diaminopimelate dehydrogenase /


Mass: 33312.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Symbiobacterium thermophilum (bacteria)
Strain: T / IAM 14863 / Gene: meso-dapdh, STH1425 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q67PI3, diaminopimelate dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1143 / 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: 2.42 Å3/Da / Density % sol: 49.14 % / Mosaicity: 1.017 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MPD, Glycerol, NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 71273 / Num. obs: 71273 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.058 / Χ2: 2.037 / Net I/σ(I): 21.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.93-1.967.50.19834871.322197.5
1.96-28.20.18635281.476199.3
2-2.048.20.17335211.651199.4
2.04-2.088.30.15735361.928199.4
2.08-2.128.30.14635662.001199.7
2.12-2.178.40.1335522.3199.7
2.17-2.238.40.1235402.041199.8
2.23-2.298.60.10735702.016199.9
2.29-2.368.60.09535561.824199.9
2.36-2.438.70.08635681.7221100
2.43-2.528.70.07735581.5671100
2.52-2.628.70.06835841.6511100
2.62-2.748.80.06135411.6351100
2.74-2.888.80.05535781.6851100
2.88-3.068.80.0535681.7611100
3.06-3.38.80.04635742.0021100
3.3-3.638.90.04335912.3371100
3.63-4.168.90.04335822.7581100
4.16-5.248.90.04636253.2271100
5.24-508.70.04736483.5371100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIO

3bio


Resolution: 1.93→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8809 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 3566 5 %RANDOM
Rwork0.1712 ---
all-71273 --
obs-70115 98.1 %-
Solvent computationBsol: 59.7918 Å2
Displacement parametersBiso max: 82.86 Å2 / Biso mean: 26.3739 Å2 / Biso min: 9.48 Å2
Baniso -1Baniso -2Baniso -3
1-4.621 Å20 Å2-2.61 Å2
2---2.651 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6777 0 60 1143 7980
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1891.5
X-RAY DIFFRACTIONc_scbond_it2.1682
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scangle_it3.1422.5
Refine LS restraints NCSRms: 0 / Type: restrain / Weight: 300
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3gol.param

+
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