[English] 日本語
Yorodumi
- PDB-9rb2: Crystal Structure of glxR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rb2
TitleCrystal Structure of glxR
ComponentsProbable oxidoreductase
KeywordsTRANSFERASE / GlxR / tartronate semialdehyde reductase / glyoxylate
Function / homology
Function and homology information


2-hydroxy-3-oxopropionate reductase activity / glyoxylate metabolic process / NAD binding / NADP binding
Similarity search - Function
2-hydroxy-3-oxopropionate reductase / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Probable oxidoreductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsParkhill, S. / little, O. / Wang, M. / Askenasy, I. / Brear, P. / Cai, W. / Welch, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2023-074 United Kingdom
CitationJournal: Microbiology (Reading, Engl.) / Year: 2025
Title: An allantoin-inducible glyoxylate utilization pathway in Pseudomonas aeruginosa.
Authors: Parkhill, S.L. / Little, O. / Askenasy, I. / Labrini, E. / Wang, M. / Brear, P.D. / Cai, W. / Deingruber, T. / Yang, T. / Spring, D.R. / Welch, M.
History
DepositionMay 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable oxidoreductase
B: Probable oxidoreductase
C: Probable oxidoreductase
D: Probable oxidoreductase


Theoretical massNumber of molelcules
Total (without water)131,9624
Polymers131,9624
Non-polymers00
Water6,503361
1
A: Probable oxidoreductase
B: Probable oxidoreductase

A: Probable oxidoreductase
B: Probable oxidoreductase


Theoretical massNumber of molelcules
Total (without water)131,9624
Polymers131,9624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area15640 Å2
ΔGint-86 kcal/mol
Surface area39960 Å2
MethodPISA
2
C: Probable oxidoreductase

C: Probable oxidoreductase

D: Probable oxidoreductase

D: Probable oxidoreductase


Theoretical massNumber of molelcules
Total (without water)131,9624
Polymers131,9624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_656-x+3/2,y+1/2,-z+11
Buried area15460 Å2
ΔGint-98 kcal/mol
Surface area39560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.176, 109.209, 146.695
Angle α, β, γ (deg.)90.00, 93.39, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Probable oxidoreductase


Mass: 32990.609 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA1500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I3L2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 25 %v/v PEGSM, 0.1 M Na Acet 4.5 pH

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.21→73.22 Å / Num. obs: 61556 / % possible obs: 98.7 % / Redundancy: 7.2 % / CC1/2: 0.978 / Rmerge(I) obs: 0.446 / Rpim(I) all: 0.178 / Rrim(I) all: 0.481 / Net I/σ(I): 4.6 / Num. measured all: 441421
Reflection shellResolution: 2.21→2.25 Å / % possible obs: 97.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 2.809 / Num. measured all: 22669 / Num. unique obs: 3061 / CC1/2: 0.351 / Rpim(I) all: 1.104 / Rrim(I) all: 3.02 / Net I/σ(I) obs: 0.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (10-JUL-2024)refinement
DIALSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→73.22 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.313 / SU Rfree Blow DPI: 0.23 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 2032 3.31 %RANDOM
Rwork0.2347 ---
obs0.236 61442 98.5 %-
Displacement parametersBiso mean: 39.49 Å2
Baniso -1Baniso -2Baniso -3
1--10.4191 Å20 Å2-2.7089 Å2
2--10.43 Å20 Å2
3----0.0108 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.21→73.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8784 0 0 361 9145
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089048HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9812254HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3138SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1588HARMONIC5
X-RAY DIFFRACTIONt_it9048HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion18.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1215SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8545SEMIHARMONIC4
LS refinement shellResolution: 2.21→2.23 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4174 -2.28 %
Rwork0.3767 1201 -
all0.3777 1229 -
obs--95.82 %

+
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