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- PDB-1yba: The active form of phosphoglycerate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1yba
TitleThe active form of phosphoglycerate dehydrogenase
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE
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 / NAD binding / identical protein binding / cytosol
Similarity search - Function
AHAS-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 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / ACT domain profile. ...AHAS-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 1 / 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 / 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
2-OXOGLUTARIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Unknown ligand / D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 Å
AuthorsThompson, J.R. / Banaszak, L.J.
Citation
Journal: Biochemistry / Year: 2005
Title: Vmax Regulation through Domain and Subunit Changes. The Active Form of Phosphoglycerate Dehydrogenase
Authors: Thompson, J.R. / Bell, J.K. / Bratt, J. / 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
DepositionDec 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)182,12024
Polymers178,4074
Non-polymers3,71320
Water24,2481346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.159, 76.159, 354.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological assembly is a tetramer consisting of the chains A, B, C, D in the asymmetric unit.

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 44601.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: serA / Plasmid: PSAWT / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12
References: UniProt: P08328, UniProt: P0A9T0*PLUS, phosphoglycerate dehydrogenase

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Non-polymers , 5 types, 1366 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 7 / Source method: obtained synthetically
#5: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 1346 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.18 M to 1.25 M AmSO4, 100 mM KPO4, pH 6.4, 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: 0.9537,0.9795,0.9797
DetectorType: SBC / Detector: CCD / Date: Dec 12, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97951
30.97971
ReflectionResolution: 2.24→50 Å / Num. all: 92508 / Num. obs: 92508 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.2
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3598 / Rsym value: 0.45 / % possible all: 77.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: Resolve PDB output based on MAD phasing

Resolution: 2.24→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.735 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.221
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23512 4538 5 %RANDOM
Rwork0.18648 ---
all0.18891 96093 --
obs0.18891 85989 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.59 Å2
Refine analyzeLuzzati coordinate error obs: 0.383 Å
Refinement stepCycle: LAST / Resolution: 2.24→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12308 0 311 1346 13965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02212908
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211841
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.99917527
X-RAY DIFFRACTIONr_angle_other_deg0.836327604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53451636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49724.991531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.537152174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0941561
X-RAY DIFFRACTIONr_chiral_restr0.0810.22016
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022340
X-RAY DIFFRACTIONr_nbd_refined0.2160.22806
X-RAY DIFFRACTIONr_nbd_other0.1870.212699
X-RAY DIFFRACTIONr_nbtor_refined0.1790.26196
X-RAY DIFFRACTIONr_nbtor_other0.090.28261
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.21077
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0530.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.232
X-RAY DIFFRACTIONr_mcbond_it0.7671.59552
X-RAY DIFFRACTIONr_mcbond_other0.1281.53340
X-RAY DIFFRACTIONr_mcangle_it1.004212988
X-RAY DIFFRACTIONr_scbond_it1.89235233
X-RAY DIFFRACTIONr_scangle_it3.0134.54539
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.545 182 -
Rwork0.51 3929 -
obs--58.14 %
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)
11.79310.1849-0.00272.0810.50982.2735-0.00350.2371-0.08850.09930.08370.1079-0.0317-0.2372-0.0803-0.1810.00930.0127-0.0195-0.046-0.2893-9.49-7.245-36.037
26.73490.99181.30052.87170.66963.1623-0.29791.1329-0.199-0.53920.7616-0.5676-0.22170.9359-0.46370.0273-0.19450.0430.3324-0.3209-0.1205-4.123-32.402-58.293
32.1418-1.118-0.58245.11360.67795.765-0.02010.2891-0.3343-0.18510.1562-0.07590.43610.3788-0.136-0.0557-0.0684-0.06380.0107-0.0915-0.1794-22.984-45.174-64.639
41.0346-0.08070.06872.0770.32562.9450.13430.1106-0.29550.45810.1489-0.48030.34650.5599-0.2832-0.06790.0633-0.14760.0098-0.1669-0.052910.501-13.882-24.117
54.3342-0.18461.11883.3793-1.26324.79160.0044-0.04260.3858-0.01110.0376-0.2195-0.30380.3223-0.042-0.08680.024-0.0025-0.1883-0.0758-0.27373.6039.829-0.566
64.52440.8924-0.0244.9881.12645.60810.1334-0.02320.21350.43390.0416-0.3348-0.38070.3419-0.1750.08510.0427-0.1208-0.1649-0.0565-0.26196.0223.71421.801
71.54210.13720.00321.7636-0.28321.4206-0.0182-0.01280.20470.02940.08180.0661-0.3742-0.1494-0.06360.00790.08640.001-0.13810.0106-0.298-27.183-29.0620.35
83.59330.77720.77046.10221.27674.09570.0872-0.413-0.39810.87460.0498-0.27150.4755-0.061-0.1370.1190.083-0.1052-0.1696-0.0121-0.1833-0.615-32.16822.068
94.1415-1.058-1.47422.8707-0.22935.74320.0048-0.4064-0.14450.4689-0.0124-0.64830.13790.68810.00750.11780.1017-0.1884-0.0904-0.0607-0.109611.765-12.80527.399
101.7379-0.9317-0.12941.3738-0.10591.78420.02920.1561-0.0199-0.29460.0198-0.04970.0940.0036-0.049-0.02250.0051-0.0003-0.1904-0.0078-0.3002-18.671-48.066-12.013
114.29490.5986-2.08774.9620.17949.1922-0.2751-0.0259-0.0538-0.05180.28160.58520.6676-1.4848-0.0065-0.0119-0.0842-0.0590.16650.0916-0.2264-44.512-41.472-35.241
124.44520.81421.31873.3384-1.67218.047-0.03590.0684-0.1504-0.12710.18810.19070.5614-0.8399-0.1522-0.0102-0.132-0.01360.0309-0.0194-0.2909-39.371-41.08-58.173
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A107 - 302
2X-RAY DIFFRACTION2A5 - 106
3X-RAY DIFFRACTION2A303 - 327
4X-RAY DIFFRACTION3A328 - 410
5X-RAY DIFFRACTION4B107 - 302
6X-RAY DIFFRACTION5B5 - 106
7X-RAY DIFFRACTION5B303 - 327
8X-RAY DIFFRACTION6B328 - 410
9X-RAY DIFFRACTION7C107 - 302
10X-RAY DIFFRACTION8C5 - 106
11X-RAY DIFFRACTION8C303 - 327
12X-RAY DIFFRACTION9C328 - 410
13X-RAY DIFFRACTION10D107 - 302
14X-RAY DIFFRACTION11D5 - 106
15X-RAY DIFFRACTION11D303 - 327
16X-RAY DIFFRACTION12D328 - 410

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