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- PDB-4hy3: Crystal structure of a phosphoglycerate oxidoreductase from rhizo... -

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Basic information

Entry
Database: PDB / ID: 4hy3
TitleCrystal structure of a phosphoglycerate oxidoreductase from rhizobium etli
Componentsphosphoglycerate oxidoreductase
KeywordsOXIDOREDUCTASE / PSI-BIOLOGY / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / Amino acid transport and metabolism / NAD binding domain. / New York Structural Genomics Research Consortium / NYSGRC / ROSSMANN FOLD / phosphoglycerate oxidoreductase
Function / homology
Function and homology information


hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable phosphoglycerate oxidoreductase protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a phosphoglycerate oxidoreductase from rhizobium etli
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionNov 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)161,8204
Polymers161,8204
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-50 kcal/mol
Surface area52490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.733, 121.118, 106.652
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTETRAMER

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Components

#1: Protein
phosphoglycerate oxidoreductase


Mass: 40455.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42 / Gene: RHE_PB00144 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2K273
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% PEG 6000, 0.1M HEPES, 0.1M MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2012 / Details: MIRRORS
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→104.55 Å / Num. all: 37449 / Num. obs: 37449 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.8 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1 / Num. unique all: 3663 / % possible all: 98.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→104.55 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.863 / SU B: 16.25 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1865 5 %RANDOM
Rwork0.204 ---
obs0.208 35562 98.9 %-
all-35562 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å21.33 Å2
2--2.33 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.8→104.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9638 0 0 156 9794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199817
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.99513284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27251256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07422.778432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.52151510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.91415102
X-RAY DIFFRACTIONr_chiral_restr0.1160.21497
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217482
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.802→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 117 -
Rwork0.281 2492 -
obs--96.31 %

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