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- PDB-2p9e: Crystal Structure of G336V mutant of E.coli phosphoglycerate dehy... -

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Basic information

Entry
Database: PDB / ID: 2p9e
TitleCrystal Structure of G336V mutant of E.coli phosphoglycerate dehydrogenase
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / G336V mutant / phosphoglycerate dehydrogenase / serine biosynthesis
Function / homology
Function and homology information


(S)-2-hydroxyglutarate dehydrogenase activity / 2-oxoglutarate reductase / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / serine binding / NADH binding / L-serine biosynthetic process / NAD+ binding / identical protein binding / cytosol
Similarity search - Function
: / AHAS small subunit-like ACT domain / : / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 ...: / AHAS small subunit-like ACT domain / : / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / ACT domain profile. / ACT domain / 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 / ACT-like domain / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PHOSPHATE ION / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDey, S. / Sacchettini, J.C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Effect of Hinge Mutations on Effector Binding and Domain Rotation in Escherichia coli D-3-Phosphoglycerate Dehydrogenase
Authors: Dey, S. / Hu, Z. / Xu, X.L. / Sacchettini, J.C. / Grant, G.A.
History
DepositionMar 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq_dif ...database_2 / struct_ref_seq_dif / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)181,23223
Polymers176,5624
Non-polymers4,67019
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22050 Å2
ΔGint-125 kcal/mol
Surface area64070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.237, 76.237, 353.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
D-3-phosphoglycerate dehydrogenase / PGDH


Mass: 44140.449 Da / Num. of mol.: 4 / Mutation: G336V, C81A, C83A, C250A, C282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: serA / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P0A9T0, phosphoglycerate dehydrogenase

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Non-polymers , 5 types, 101 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.5M AmSO4, 0.1M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2005 / Details: Monochromator
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 61423 / % possible obs: 99.5 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 19.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.64 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PA3

2pa3


Resolution: 2.6→35 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.87 / SU B: 13.507 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.705 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27923 3105 5.1 %RANDOM
Rwork0.2061 ---
obs0.2098 58183 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.904 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å20 Å2
2--2.27 Å20 Å2
3----4.53 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12267 0 299 82 12648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212779
X-RAY DIFFRACTIONr_angle_refined_deg1.921.99917370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83951615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62624.952523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.398152140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2381560
X-RAY DIFFRACTIONr_chiral_restr0.1210.22009
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029484
X-RAY DIFFRACTIONr_nbd_refined0.2810.36142
X-RAY DIFFRACTIONr_nbtor_refined0.3420.58571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.5839
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4340.51
X-RAY DIFFRACTIONr_mcbond_it4.0358185
X-RAY DIFFRACTIONr_mcangle_it5.998712860
X-RAY DIFFRACTIONr_scbond_it8.02395000
X-RAY DIFFRACTIONr_scangle_it10.225114510
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 212 -
Rwork0.312 4104 -
obs-4104 94.61 %

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