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- PDB-2p9c: Crystal structure of serine bound G336V mutant of E.coli phosphog... -

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Basic information

Entry
Database: PDB / ID: 2p9c
TitleCrystal structure of serine bound G336V mutant of E.coli phosphoglycerate dehydrogenase
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / phosphoglycerate dehydrogenase
Function / homology
Function and homology information


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
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 dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / ACT domain profile. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic 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 dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / ACT domain profile. / ACT domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / ACT-like 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 / 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: 2.46 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 24, 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: Advisory / Derived calculations / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8226
Polymers88,2812
Non-polymers1,5414
Water97354
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)179,64412
Polymers176,5624
Non-polymers3,0828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area19840 Å2
ΔGint-79 kcal/mol
Surface area63210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.142, 130.785, 50.188
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: 44140.449 Da / Num. of mol.: 2 / 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
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


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


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


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG3000, 0.1M cacodylate, 0.2M MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.46→35 Å / Num. obs: 31001 / % possible obs: 88.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 20.2
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3604 / % possible all: 72.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PA3

2pa3


Resolution: 2.46→35 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.898 / SU B: 18.873 / SU ML: 0.244 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.698 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28059 1556 5 %RANDOM
Rwork0.21894 ---
obs0.22204 29392 88.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.721 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2---2.76 Å20 Å2
3---4.33 Å2
Refinement stepCycle: LAST / Resolution: 2.46→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6140 0 102 54 6296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226354
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9918630
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9524.962262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.637151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1871530
X-RAY DIFFRACTIONr_chiral_restr0.0890.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.32789
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.54358
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.5374
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.357
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3260.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.954111
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.38976448
X-RAY DIFFRACTIONr_scbond_it5.94292442
X-RAY DIFFRACTIONr_scangle_it7.547112182
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 --
Rwork0.291 1704 -
obs--70.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5905-0.17270.39374.3302-1.10773.85250.05120.36180.0959-0.39510.17690.5885-0.0302-0.5294-0.22810.02910.00030.0134-0.06470.02710.0012-33.6913-24.67725.4762
21.2688-0.5605-0.03561.6870.02131.4569-0.0685-0.1533-0.11550.10120.0585-0.1210.10340.1390.01-0.06060.0005-0.002-0.15850.0106-0.0632-23.46010.633728.4783
32.99811.52530.4511.06750.85781.42290.01050.3946-0.201-0.42220.0432-0.2286-0.0746-0.2182-0.05370.06380.03820.0508-0.13470.03870.0449-23.1295-47.397311.1192
42.61520.7509-1.46952.1783-0.90791.50260.0258-0.25620.32730.08640.04080.6020.0293-0.1717-0.0667-0.0993-0.0262-0.003-0.0332-0.04710.1586-10.220939.581430.5436
50.4304-0.2105-0.57521.3462-0.21971.48450.0920.12140.0369-0.2923-0.073-0.1994-0.06710.1844-0.0190.0691-0.04120.0651-0.1216-0.0014-0.0356-19.923914.34597.7541
62.2894-1.1582-0.43421.65491.82452.72960.1444-0.4940.28450.12030.04270.17830.1251-0.0741-0.1871-0.0547-0.0605-0.0369-0.1049-0.03450.047312.373250.842825.4795
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1077 - 107
2X-RAY DIFFRACTION2AA108 - 294108 - 294
3X-RAY DIFFRACTION3AA337 - 410337 - 410
4X-RAY DIFFRACTION4BB7 - 1077 - 107
5X-RAY DIFFRACTION5BB108 - 294108 - 294
6X-RAY DIFFRACTION6BB337 - 410337 - 410

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