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- PDB-4s1v: Crystal structure of phosphoglycerate oxidoreductase from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 4s1v
TitleCrystal structure of phosphoglycerate oxidoreductase from Vibrio Cholerae o395
ComponentsD-3-phosphoglycerate dehydrogenase-related protein
KeywordsOXIDOREDUCTASE / ROSSMAN FOLD
Function / homology
Function and homology information


phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / 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
D-3-phosphoglycerate dehydrogenase-related protein / D-isomerspecific 2-hydroxyacid dehydrogenase family protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTarique, K.F. / Rehman, S.A.A. / Devi, S. / Gourinath, S.
CitationJournal: To be Published
Title: Crystal Structure of Phosphoglycerate Oxidoreductase from Vibrio Cholerae O395
Authors: Tarique, K.F. / Rehman, S.A.A. / Devi, S. / Gourinath, S.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: D-3-phosphoglycerate dehydrogenase-related protein
A: D-3-phosphoglycerate dehydrogenase-related protein
B: D-3-phosphoglycerate dehydrogenase-related protein
C: D-3-phosphoglycerate dehydrogenase-related protein


Theoretical massNumber of molelcules
Total (without water)146,4754
Polymers146,4754
Non-polymers00
Water8,179454
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: D-3-phosphoglycerate dehydrogenase-related protein
C: D-3-phosphoglycerate dehydrogenase-related protein


Theoretical massNumber of molelcules
Total (without water)73,2382
Polymers73,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-40 kcal/mol
Surface area25150 Å2
MethodPISA
3
A: D-3-phosphoglycerate dehydrogenase-related protein
B: D-3-phosphoglycerate dehydrogenase-related protein


Theoretical massNumber of molelcules
Total (without water)73,2382
Polymers73,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-41 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.916, 83.258, 85.986
Angle α, β, γ (deg.)64.39, 81.94, 76.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
D-3-phosphoglycerate dehydrogenase-related protein / D-isomerspecific 2-hydroxyacid dehydrogenase family protein


Mass: 36618.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O395 / Gene: VC0395_0573, VC395_A0682 / Plasmid: PET21(C) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5F016, UniProt: A0A0H2UKZ7*PLUS, phosphoglycerate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 10% PEG 3350, 10% ISOPROPANOL (V/V), 0.3M LICL, 0.1M SODIUM CITRATE, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 70407 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rsym value: 0.108 / Net I/σ(I): 15.86
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.69 / Rsym value: 0.578 / % possible all: 92.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3GG9

3gg9


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.968 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3549 5 %RANDOM
Rwork0.202 ---
obs0.204 66853 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å2-0.05 Å2-0.05 Å2
2---0.16 Å20.08 Å2
3----0.56 Å2
Refine analyzeLuzzati coordinate error obs: 0.266 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9744 0 0 454 10198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01910003
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.96513599
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19551259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.824.318447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.696151668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9281559
X-RAY DIFFRACTIONr_chiral_restr0.0690.21546
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217587
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 254 -
Rwork0.285 4765 -
obs--91.35 %

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