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- PDB-9rfa: Apo structure of glxR -

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Basic information

Entry
Database: PDB / ID: 9rfa
TitleApo structure of glxR
ComponentsProbable oxidoreductase
KeywordsHYDROLASE / Fragment based drug discovery / kinase
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: 2.069 Å
AuthorsBrear, P. / Parkhill, S. / Wang, M. / Askenasy, I. / Cai, W. / Welch, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private 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
DepositionJun 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-82 kcal/mol
Surface area39880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.442, 121.465, 132.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18 %v/v PEGSH 0.2 M (NH4)2SO4, 0.1 M ADA 6.5 pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.069→60.73 Å / Num. obs: 80069 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.061 / Rrim(I) all: 0.227 / Net I/σ(I): 6.7
Reflection shellResolution: 2.07→2.1 Å / % possible obs: 99.1 % / Redundancy: 13.4 % / Rmerge(I) obs: 4.611 / Num. measured all: 52372 / Num. unique obs: 3916 / CC1/2: 0.402 / Rpim(I) all: 1.301 / Rrim(I) all: 4.793 / Net I/σ(I) obs: 0.3

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (10-JUL-2024)refinement
DIALSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.069→60.73 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.251 / SU Rfree Blow DPI: 0.217 / SU Rfree Cruickshank DPI: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.315 1975 2.58 %RANDOM
Rwork0.2701 ---
obs0.2712 76426 95.5 %-
Displacement parametersBiso mean: 58.93 Å2
Baniso -1Baniso -2Baniso -3
1--13.7692 Å20 Å20 Å2
2--16.6723 Å20 Å2
3----2.9032 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.069→60.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8709 0 5 44 8758
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088856HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0411974HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3057SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1544HARMONIC5
X-RAY DIFFRACTIONt_it8856HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion19.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1196SEMIHARMONIC5
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_contact7409SEMIHARMONIC4
LS refinement shellResolution: 2.07→2.09 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4975 -2.75 %
Rwork0.4559 1487 -
all0.457 1529 -
obs--62.22 %

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