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- PDB-1ygy: Crystal Structure of D-3-Phosphoglycerate dehydrogenase From Myco... -

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Basic information

Entry
Database: PDB / ID: 1ygy
TitleCrystal Structure of D-3-Phosphoglycerate dehydrogenase From Mycobacterium tuberculosis
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / Phosphoglycerate dehydrogenase / serine biosynthesis / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


2-oxoglutarate reductase / phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / L-serine biosynthetic process / peptidoglycan-based cell wall / NAD binding / plasma membrane
Similarity search - Function
D-3-phosphoglycerate dehydrogenase; domain 3 / D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / 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-3-phosphoglycerate dehydrogenase; domain 3 / D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase, ASB domain / D-3-phosphoglycerate dehydrogenase intervening domain / Allosteric substrate binding domain superfamily / 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 / 60s Ribosomal Protein L30; Chain: A; / 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
L(+)-TARTARIC ACID / D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDey, S. / Grant, G.A. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of Mycobacterium tuberculosis D-3-Phosphoglycerate Dehydrogenase: EXTREME ASYMMETRY IN A TETRAMER OF IDENTICAL SUBUNITS
Authors: Dey, S. / Grant, G.A. / Sacchettini, J.C.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: D-3-Phosphoglycerate Dehydrogenase from Mycobacterium tuberculosis Is a Link between the Escherichia coli and Mammalian Enzymes
Authors: Dey, S. / Hu, Z. / Xu, X.L. / Sacchettini, J.C. / Grant, G.A.
History
DepositionJan 5, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 2.0Jul 10, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Remark 650HELIX Determination method: Author determined

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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)109,8605
Polymers109,4102
Non-polymers4503
Water5,675315
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)219,72110
Polymers218,8204
Non-polymers9016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area18980 Å2
ΔGint-58 kcal/mol
Surface area78960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)165.513, 165.513, 218.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsBiological assembly is a tetramer generated from the dimer in the asymmetric unit

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Components

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


Mass: 54705.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: serA1 / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A544, UniProt: P9WNX3*PLUS, phosphoglycerate dehydrogenase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium potassium tartrate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-D10.97937, 0.97961
SYNCHROTRONAPS 14-BM-C20.9
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 14, 2003
ADSC QUANTUM 3152CCDJul 7, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.979611
30.91
ReflectionResolution: 2.3→50 Å / Num. obs: 78223 / % possible obs: 99.7 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 24.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 4.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→48.8 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.767 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24853 3918 5 %RANDOM
Rwork0.20496 ---
obs0.20715 74263 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.302 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å21.36 Å20 Å2
2--2.72 Å20 Å2
3----4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7672 0 30 315 8017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217807
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.97610668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20251052
X-RAY DIFFRACTIONr_chiral_restr0.1140.21330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025844
X-RAY DIFFRACTIONr_nbd_refined0.2550.33683
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5699
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.391
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.523
X-RAY DIFFRACTIONr_mcbond_it3.18355228
X-RAY DIFFRACTIONr_mcangle_it4.82678368
X-RAY DIFFRACTIONr_scbond_it6.57492579
X-RAY DIFFRACTIONr_scangle_it8.932112300
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 269
Rwork0.313 5420
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)
10.7793-1.3882-0.03373.78370.58273.2133-0.2828-0.23830.25860.39090.1837-0.2320.0473-0.01150.09910.43540.1958-0.07730.1933-0.00740.276546.69339.918626.0118
20.43350.0778-0.41310.960.74252.33410.0193-0.02230.13320.2898-0.0753-0.0110.5315-0.60730.0560.2873-0.0449-0.0160.34480.01530.227919.966350.50377.5942
30.057-0.17630.56650.50850.80473.46780.04910.0242-0.03420.0540.04370.00580.15820.0567-0.09280.15430.102-0.00380.25430.00160.338236.199466.787136.552
41.6348-0.82750.76663.36980.66154.52550.10430.56080.0511-0.1204-0.3184-0.1657-0.081-0.48260.21410.0110.06810.02980.53080.02480.311913.587570.182140.3372
53.08811.0402-1.07431.0006-0.73683.3405-0.13360.5495-0.0431-0.07970.2172-0.0320.281-0.6144-0.08370.1215-0.0229-0.03230.483-0.00130.23038.596353.234-28.6747
60.60060.253-0.34750.68650.14472.5625-0.03830.10030.0633-0.02580.0323-0.13730.78890.00990.00590.41190.1186-0.03910.1618-0.02670.26133.27541.7226-10.0593
70.98930.8431-0.34752.4120.60583.152-0.07320.0986-0.0046-0.30840.07240.1273-0.446-0.30870.00080.21520.1356-0.00680.2488-0.00180.28529.765575.8899-31.0001
81.8735-0.77751.53083.48880.42911.66580.15710.2532-0.235-0.4167-0.07330.0098-0.3290.0663-0.08380.36470.21440.03380.1816-0.03310.331324.869395.7962-21.618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 993 - 99
2X-RAY DIFFRACTION1AA283 - 319283 - 319
3X-RAY DIFFRACTION2AA100 - 282100 - 282
4X-RAY DIFFRACTION3AA320 - 454320 - 454
5X-RAY DIFFRACTION4AA455 - 529455 - 529
6X-RAY DIFFRACTION5BB3 - 993 - 99
7X-RAY DIFFRACTION5BB283 - 319283 - 319
8X-RAY DIFFRACTION6BB100 - 282100 - 282
9X-RAY DIFFRACTION7BB320 - 454320 - 454
10X-RAY DIFFRACTION8BB455 - 529455 - 529

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