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- PDB-3ddn: Crystal structure of hydroxypyruvic acid phosphate bound D-3-phos... -

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Basic information

Entry
Database: PDB / ID: 3ddn
TitleCrystal structure of hydroxypyruvic acid phosphate bound D-3-phosphoglycerate dehydrogenase in mycobacterium tuberculosis
ComponentsD-3-phosphoglycerate dehydrogenase
KeywordsOXIDOREDUCTASE / phosphoglycerate dehydrogenase / serine biosynthesis / Amino-acid biosynthesis / NAD
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-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 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 / 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
2-oxo-3-(phosphonooxy)propanoic acid / L(+)-TARTARIC ACID / D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2.4 Å
AuthorsDey, S. / Sacchettini, J.C.
CitationJournal: Biochemistry / Year: 2008
Title: Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase
Authors: Dey, S. / Burton, R.L. / Grant, G.A. / Sacchettini, J.C.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: 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_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 1.3Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7826
Polymers109,1482
Non-polymers6344
Water2,972165
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)219,56412
Polymers218,2954
Non-polymers1,2698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area19150 Å2
ΔGint-51 kcal/mol
Surface area77980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.601, 165.601, 218.299
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 54573.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: serA1 / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A544, UniProt: P9WNX3*PLUS, phosphoglycerate dehydrogenase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-HPV / 2-oxo-3-(phosphonooxy)propanoic acid / Hydroxypyruvic acid phosphate


Mass: 184.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
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: 3.96 Å3/Da / Density % sol: 68.93 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→48.8 Å / Num. obs: 69375 / % possible obs: 100 % / Redundancy: 21.6 % / Rsym value: 0.038 / Net I/σ(I): 26
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 22.3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
XFITdata reduction
RefinementMethod to determine structure: refinement
Starting model: 1YGY

1ygy


Resolution: 2.4→48.79 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.866 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24399 3485 5 %RANDOM
Rwork0.20376 ---
obs0.20579 65806 99.96 %-
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: 43.123 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å21.43 Å20 Å2
2--2.86 Å20 Å2
3----4.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7659 0 41 165 7865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227828
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.98310695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg51049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.281299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg151215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1557
X-RAY DIFFRACTIONr_chiral_restr0.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.025857
X-RAY DIFFRACTIONr_nbd_refined0.33586
X-RAY DIFFRACTIONr_nbtor_refined0.55366
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.5612
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.388
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.518
X-RAY DIFFRACTIONr_mcbond_it55281
X-RAY DIFFRACTIONr_mcangle_it78360
X-RAY DIFFRACTIONr_scbond_it92715
X-RAY DIFFRACTIONr_scangle_it112335
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 240 -
Rwork0.258 4764 -
obs--100 %
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)
10.02650.0555-0.07450.28830.24911.16390.0106-0.0685-0.07770.0728-0.02720.01820.299-0.16770.0167-0.07120.0253-0.0035-0.0510.0006-0.016529.81954.990624.3564
20.50110.04450.05560.7834-0.0161.0674-0.01280.1076-0.0278-0.1450.03580.07010.1204-0.1514-0.023-0.15610.06320.0106-0.0597-0.0357-0.088425.219361.133-21.513
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 5293 - 528
2X-RAY DIFFRACTION2BB4 - 5293 - 528

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