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- PDB-3evt: Crystal structure of phosphoglycerate dehydrogenase from Lactobac... -

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Basic information

Entry
Database: PDB / ID: 3evt
TitleCrystal structure of phosphoglycerate dehydrogenase from Lactobacillus plantarum
ComponentsPhosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / DEHYDROGENASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / 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, 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
2-hydroxyacid dehydrogenase / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBonanno, J.B. / Gilmore, M. / Bain, K.T. / Do, J. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of phosphoglycerate dehydrogenase from Lactobacillus plantarum
Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Do, J. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)35,2771
Polymers35,2771
Non-polymers00
Water1,60389
1
A: Phosphoglycerate dehydrogenase

A: Phosphoglycerate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)70,5542
Polymers70,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4750 Å2
ΔGint-27 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.848, 75.848, 107.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsprobable dimer

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Components

#1: Protein Phosphoglycerate dehydrogenase


Mass: 35277.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: lp_2790, serA3 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q88TW9, UniProt: F9URQ7*PLUS, phosphoglycerate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Hepes pH 7.5, 8% ethylene glycol, 20% PEG 10K, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.2→37.932 Å / Num. all: 16646 / Num. obs: 16646 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.9 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 20.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 22.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 7.6 / Num. measured all: 52414 / Num. unique all: 2365 / Rsym value: 0.37 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.38 / WRfactor Rwork: 0.275 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.725 / SU B: 7.55 / SU ML: 0.189 / SU R Cruickshank DPI: 0.325 / SU Rfree: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.325 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 814 4.9 %RANDOM
Rwork0.23 ---
obs0.232 16565 100 %-
all-16565 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.36 Å2 / Biso mean: 52.627 Å2 / Biso min: 26.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 0 89 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222391
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9363280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85924.84899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75115352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.766158
X-RAY DIFFRACTIONr_chiral_restr0.1080.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211816
X-RAY DIFFRACTIONr_mcbond_it0.9011.51549
X-RAY DIFFRACTIONr_mcangle_it1.66722496
X-RAY DIFFRACTIONr_scbond_it2.6283842
X-RAY DIFFRACTIONr_scangle_it4.1024.5784
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 62 -
Rwork0.311 1106 -
all-1168 -
obs-1106 100 %

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