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- PDB-2p9g: Crystal structure of serine bound G336V,G337V double mutant of E.... -

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Basic information

Entry
Database: PDB / ID: 2p9g
TitleCrystal structure of serine bound G336V,G337V double mutant of E.coli phosphoglycerate dehydrogenase
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / serine biosynthesis / D-3-phosphoglycerate dehydrogenase / double mutation
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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: 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
B: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9066
Polymers88,3652
Non-polymers1,5414
Water88349
1
A: D-3-phosphoglycerate dehydrogenase
B: D-3-phosphoglycerate dehydrogenase
hetero molecules

A: D-3-phosphoglycerate dehydrogenase
B: D-3-phosphoglycerate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,81212
Polymers176,7304
Non-polymers3,0828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area19500 Å2
ΔGint-78 kcal/mol
Surface area62520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)144.072, 132.239, 52.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 44182.527 Da / Num. of mol.: 2 / Mutation: C81A, C83A, C250A, C282A, G336V, G337V
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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% PEG 400, 0.1M acetate, 0.2M Calcium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 9, 2006 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.8→40.32 Å / Num. obs: 25289 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PSD

1psd


Resolution: 2.8→35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.366 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25008 1285 5.1 %RANDOM
Rwork0.19737 ---
obs0.20004 23997 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.721 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å20 Å20 Å2
2---3 Å20 Å2
3---6.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 0 102 49 6281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226344
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.998618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97124.962262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.899151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8791530
X-RAY DIFFRACTIONr_chiral_restr0.1120.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024710
X-RAY DIFFRACTIONr_nbd_refined0.2740.32887
X-RAY DIFFRACTIONr_nbtor_refined0.3440.54346
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.5406
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.3126
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.524
X-RAY DIFFRACTIONr_mcbond_it4.07454096
X-RAY DIFFRACTIONr_mcangle_it6.24476440
X-RAY DIFFRACTIONr_scbond_it8.10192434
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 107 -
Rwork0.294 1732 -
obs--100 %

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