[English] 日本語
Yorodumi
- PDB-2bhq: Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bhq
TitleCrystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound product glutamate.
Components1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / 1-PYRROLINE-5-CARBOXYLATE / DEHYROGENASE / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


L-glutamate gamma-semialdehyde dehydrogenase / L-glutamate gamma-semialdehyde dehydrogenase activity / L-proline catabolic process to L-glutamate / cytoplasmic side of plasma membrane / nucleotide binding
Similarity search - Function
1-pyrroline-5-carboxylate dehydrogenase / : / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. ...1-pyrroline-5-carboxylate dehydrogenase / : / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GLUTAMIC ACID / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsInagaki, E. / Tahirov, T.H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase.
Authors: Inagaki, E. / Ohshima, N. / Takahashi, H. / Kuroishi, C. / Yokoyama, S. / Tahirov, T.H.
History
DepositionJan 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
B: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,70415
Polymers114,2282
Non-polymers1,47613
Water24,0681336
1
A: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
B: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
hetero molecules

A: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
B: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
hetero molecules

A: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
B: 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,11145
Polymers342,6836
Non-polymers4,42839
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.618, 102.618, 279.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-2073-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9778, -0.20933, -0.00891), (-0.20934, -0.97784, 5.0E-5), (-0.00872, 0.00182, -0.99996)
Vector: 8.30915, 69.28711, 223.0739)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE


Mass: 57113.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SI02, EC: 1.5.1.12

-
Non-polymers , 5 types, 1349 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1336 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.2
Details: PROTEIN WAS CRYSTALLIZED FROM 32% MPD, 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN SATURATED GLUTAMATE.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Dec 1, 2002 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 255946 / % possible obs: 95 % / Observed criterion σ(I): -0.5 / Redundancy: 2.8 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 90.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UZB

1uzb


Resolution: 1.4→29.62 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 709699.17 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.186 10194 5 %RANDOM
Rwork0.17 ---
obs0.17 204948 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.4013 Å2 / ksol: 0.32425 e/Å3
Displacement parametersBiso mean: 12.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20.8 Å20 Å2
2--1.14 Å20 Å2
3----2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.4→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8070 0 100 1336 9506
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.831.5
X-RAY DIFFRACTIONc_mcangle_it1.182
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 1634 5 %
Rwork0.28 31175 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4SOL.PARSOL.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.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