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- PDB-1sc6: Crystal Structure of W139G D-3-Phosphoglycerate dehydrogenase com... -

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Basic information

Entry
Database: PDB / ID: 1sc6
TitleCrystal Structure of W139G D-3-Phosphoglycerate dehydrogenase complexed with NAD+
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / allosteric regulation phosphoglycerate dehydrogenase PGDH
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
AuthorsBell, J.K. / Grant, G.A. / Banaszak, L.J.
Citation
Journal: Biochemistry / Year: 2004
Title: Multiconformational states in phosphoglycerate dehydrogenase
Authors: Bell, J.K. / Grant, G.A. / Banaszak, L.J.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 1995
Title: The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase
Authors: Schuller, D.J. / Grant, G.A. / Banaszak, L.J.
History
DepositionFeb 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)177,5088
Polymers174,8544
Non-polymers2,6544
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18410 Å2
ΔGint-63 kcal/mol
Surface area58300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.487, 70.842, 149.468
Angle α, β, γ (deg.)90.00, 95.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43713.555 Da / Num. of mol.: 4 / Mutation: W139G,C81A,C83A,C250A,C282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SERA, B2913, C3494, Z4251, ECS3784, SF2898, S3098 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9T0, phosphoglycerate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.37 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Citrate, PEG 4K, NAD, alpha-ketoglutarate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934, 0.97951, 0.95373
DetectorType: ANL-ECT / Detector: CCD / Date: Mar 23, 2001
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979511
30.953731
ReflectionResolution: 2.09→40 Å / Num. all: 172809 / Num. obs: 104640 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078 / Rsym value: 0.063 / Net I/σ(I): 20.6
Reflection shellResolution: 2.07→2.15 Å / Redundancy: 3 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2 / Num. unique all: 3426 / Rsym value: 0.436 / % possible all: 95.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
DMmodel building
CNSrefinement
HKL-2000data reduction
DMphasing
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.09→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 17250 -random
Rwork0.22 ---
all0.22 ---
obs0.22 104630 95.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.615 Å20 Å2-5.052 Å2
2---1.069 Å20 Å2
3---2.684 Å2
Refinement stepCycle: LAST / Resolution: 2.09→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11663 0 176 463 12302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcangle_it2.609
X-RAY DIFFRACTIONc_mcbond_it1.589
X-RAY DIFFRACTIONc_scangle_it3.314
X-RAY DIFFRACTIONc_scbond_it2.312

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