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- PDB-4nfy: Crystal Structure of 3-phosphoglycerate Dehydrogenase from Entamo... -

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Basic information

Entry
Database: PDB / ID: 4nfy
TitleCrystal Structure of 3-phosphoglycerate Dehydrogenase from Entamoeba histolytica
ComponentsD-3-phosphoglycerate dehydrogenase, putative
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenases
Function / homology
Function and homology information


phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / NAD binding / identical protein 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 putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSingh, R.K. / Gourinath, S.
CitationJournal: Febs J. / Year: 2014
Title: Crystal structures and kinetics of Type III 3-phosphoglycerate dehydrogenase reveal catalysis by lysine.
Authors: Singh, R.K. / Raj, I. / Pujari, R. / Gourinath, S.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-3-phosphoglycerate dehydrogenase, putative
B: D-3-phosphoglycerate dehydrogenase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4274
Polymers69,1832
Non-polymers2442
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-8 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.906, 85.906, 84.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein D-3-phosphoglycerate dehydrogenase, putative / D-phosphoglycerate dehydrogenase


Mass: 34591.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1-IMSS / Gene: 3-phosphoglycerate dehydrogenase, EHI_060860, EhPGDH / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76KF5, phosphoglycerate dehydrogenase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG, 100mM Tris-cl, 350mM sodium formate, 5% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.45→85.91 Å / Num. obs: 22458 / Redundancy: 4.2 % / Rsym value: 0.047 / Net I/σ(I): 36.4
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 7.4 / Rsym value: 0.202

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WWK

1wwk


Resolution: 2.45→85.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.961 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.803 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25895 1150 5.1 %RANDOM
Rwork0.19403 ---
obs0.19728 21307 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.265 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å2-0 Å2
2--2.58 Å2-0 Å2
3----5.17 Å2
Refinement stepCycle: LAST / Resolution: 2.45→85.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4730 0 16 135 4881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194803
X-RAY DIFFRACTIONr_bond_other_d0.0010.024874
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.9816421
X-RAY DIFFRACTIONr_angle_other_deg0.712311268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06725.217207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81615981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3791526
X-RAY DIFFRACTIONr_chiral_restr0.0650.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02987
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_it2.0754.5842412
X-RAY DIFFRACTIONr_mcbond_other2.0744.5812409
X-RAY DIFFRACTIONr_mcangle_it3.356.873009
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3815.0082391
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: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 85 -
Rwork0.24 1469 -
obs--93.56 %

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