[English] 日本語
Yorodumi
- PDB-1f06: THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f06
TitleTHREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE
ComponentsMESO-DIAMINOPIMELATE D-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / Enzyme-NADPH-inhibitor ternary complex
Function / homology
Function and homology information


diaminopimelate dehydrogenase / diaminopimelate dehydrogenase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate
Similarity search - Function
Diaminopimelate dehydrogenase, Ddh / Meso-diaminopimelate D-dehydrogenase, C-terminal / Diaminopimelic acid dehydrogenase C-terminal domain / 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
L-2-AMINO-6-METHYLENE-PIMELIC ACID / Chem-NDP / Meso-diaminopimelate D-dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsCirilli, M. / Scapin, G. / Sutherland, A. / Caplan, J.F. / Vederas, J.C. / Blanchard, J.S.
CitationJournal: Protein Sci. / Year: 2000
Title: The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate.
Authors: Cirilli, M. / Scapin, G. / Sutherland, A. / Vederas, J.C. / Blanchard, J.S.
History
DepositionMay 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: MESO-DIAMINOPIMELATE D-DEHYDROGENASE
B: MESO-DIAMINOPIMELATE D-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1635
Polymers70,4852
Non-polymers1,6783
Water2,090116
1
A: MESO-DIAMINOPIMELATE D-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9882
Polymers35,2421
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MESO-DIAMINOPIMELATE D-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1753
Polymers35,2421
Non-polymers9332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-37 kcal/mol
Surface area25340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.547, 65.591, 84.281
Angle α, β, γ (deg.)90.00, 106.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein MESO-DIAMINOPIMELATE D-DEHYDROGENASE


Mass: 35242.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Plasmid: PET23B / Production host: Escherichia coli (E. coli) / References: UniProt: P04964, diaminopimelate dehydrogenase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-2NP / L-2-AMINO-6-METHYLENE-PIMELIC ACID


Mass: 187.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 8000, magnesium acetate, cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %PEG80001reservoir
2200 mMmagnesium acetate1reservoir
3100 mMsodium acetate1reservoir
424 mg/mlprotein1drop
520 mMHEPES1drop
65 mMNADPH1drop
720 mML-2-amino-6-methylene-pimelate1drop

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Jul 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→48.6 Å / Num. all: 111792 / Num. obs: 111416 / % possible obs: 86.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.82 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.615
Reflection shellResolution: 2.11→2.25 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.224 / % possible all: 47.3
Reflection
*PLUS
Num. obs: 39441
Reflection shell
*PLUS
% possible obs: 67 %

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementResolution: 2.1→48.6 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.209 1027 RANDOM
Rwork0.179 --
all0.197 39428 -
obs0.185 39428 -
Refinement stepCycle: LAST / Resolution: 2.1→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 109 116 5175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.398
X-RAY DIFFRACTIONx_torsion_deg26.412
X-RAY DIFFRACTIONx_torsion_impr_deg1.332
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 48.6 Å / σ(F): 2 / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.33

+
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