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- PDB-2pa3: crystal structure of serine bound G336V mutant of E.coli phosphog... -

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Basic information

Entry
Database: PDB / ID: 2pa3
Titlecrystal structure of serine bound G336V mutant of E.coli phosphoglycerate dehydrogenase
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / SERINE / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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 27, 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: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,9113
Polymers44,1401
Non-polymers7712
Water32418
1
A: D-3-phosphoglycerate dehydrogenase
hetero molecules

A: D-3-phosphoglycerate dehydrogenase
hetero molecules

A: D-3-phosphoglycerate dehydrogenase
hetero molecules

A: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,64412
Polymers176,5624
Non-polymers3,0828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-2/31
crystal symmetry operation12_544x,x-y-1,-z-2/31
Buried area19000 Å2
ΔGint-73 kcal/mol
Surface area63830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.789, 152.789, 163.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 44140.449 Da / Num. of mol.: 1 / Mutation: C81A, C83A, C250A, C282A, G336V
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
#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% PEG1000, 0.1M Na/K phosphate, 0.2M MgCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2005 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 30270 / % possible obs: 99.9 % / Redundancy: 20.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 39.78
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 5.23 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PSD

1psd


Resolution: 2.74→35 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.615 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25336 1528 5.1 %RANDOM
Rwork0.21703 ---
obs0.2188 28694 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.607 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.74→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 50 18 3144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223195
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.994340
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0645405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82324.962133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.63415541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7881515
X-RAY DIFFRACTIONr_chiral_restr0.1150.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022373
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2690.31413
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3450.52146
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.5184
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.384
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.98952060
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.94773238
X-RAY DIFFRACTIONr_scbond_it7.73491238
X-RAY DIFFRACTIONr_scangle_it10.015111102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.74→2.809 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.541 106 -
Rwork0.413 2058 -
obs--99.49 %

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