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- PDB-3dc2: Crystal structure of serine bound D-3-phosphoglycerate dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 3dc2
TitleCrystal structure of serine bound D-3-phosphoglycerate dehydrogenase from 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
SERINE / L(+)-TARTARIC ACID / D-3-phosphoglycerate dehydrogenase / D-3-phosphoglycerate dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 3, 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 9, 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)110,0717
Polymers109,4102
Non-polymers6605
Water1,38777
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)220,14114
Polymers218,8204
Non-polymers1,32110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area19260 Å2
ΔGint-52 kcal/mol
Surface area77980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.192, 165.192, 218.894
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: 54705.059 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-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


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


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.94 Å3/Da / Density % sol: 68.78 %
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: 2.7→46.57 Å / Num. obs: 48518 / % possible obs: 99.2 % / Redundancy: 20.8 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 19.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

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

1ygy


Resolution: 2.7→46.57 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU B: 27.074 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26324 2452 5.1 %RANDOM
Rwork0.22227 ---
obs0.22433 46059 99.2 %-
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: 67.598 Å2
Baniso -1Baniso -2Baniso -3
1-5.8 Å22.9 Å20 Å2
2--5.8 Å20 Å2
3----8.7 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7640 0 44 77 7761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227786
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.98210635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg51046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.305295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg151206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1556
X-RAY DIFFRACTIONr_chiral_restr0.21326
X-RAY DIFFRACTIONr_gen_planes_refined0.025824
X-RAY DIFFRACTIONr_nbd_refined0.33788
X-RAY DIFFRACTIONr_nbtor_refined0.55411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.5566
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.397
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.514
X-RAY DIFFRACTIONr_mcbond_it55287
X-RAY DIFFRACTIONr_mcangle_it78339
X-RAY DIFFRACTIONr_scbond_it92676
X-RAY DIFFRACTIONr_scangle_it112296
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 184 -
Rwork0.364 3327 -
obs--99.24 %
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)
13.379-2.13460.75076.32210.71827.8262-0.0997-0.3840.21640.4930.026-0.15110.13470.28040.07360.08860.2158-0.0657-0.1430.0117-0.01346.445339.615825.9418
22.05270.2648-0.15843.37431.44824.12230.0498-0.2259-0.10760.3536-0.18270.37730.9309-0.84710.133-0.17750.002-0.0423-0.0636-0.0326-0.151620.012750.2877.4953
34.11340.88532.69081.93861.969710.10860.0962-0.2043-0.06410.2004-0.23480.0340.5858-0.20570.1386-0.3910.08650.0487-0.2524-0.0705-0.156836.23666.471136.6028
48.2527-3.1864-1.65786.92862.27378.37590.23230.75530.0842-0.5791-0.10880.0322-0.3732-0.5456-0.1235-0.3335-0.02840.06320.4291-0.06290.094613.552769.231840.7602
57.00320.1589-0.15261.8687-1.24968.67440.04831.1811-0.426-0.40070.24380.30680.5888-0.6442-0.2921-0.24620.0356-0.09340.2462-0.05670.03138.961952.9519-28.8249
61.71080.743-0.26923.0342-0.57744.1211-0.08010.094-0.3576-0.33580.0706-0.09911.2049-0.07740.00940.02890.2093-0.0596-0.2687-0.0607-0.142933.401441.5671-10.0189
73.7293-1.04390.98334.96520.27725.763-0.21140.01960.4181-0.66620.05050.2252-0.661-0.44230.1609-0.00750.146-0.1672-0.1122-0.0408-0.0330.41575.7257-30.4635
83.2777-1.34082.13878.9997-0.67826.67920.2760.7279-0.165-0.6168-0.1421-0.2919-0.03840.3366-0.13390.1560.307-0.0463-0.1137-0.05780.135325.011495.7837-21.763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 994 - 99
2X-RAY DIFFRACTION1AA283 - 319283 - 319
3X-RAY DIFFRACTION2AA100 - 282100 - 282
4X-RAY DIFFRACTION3AA320 - 454320 - 454
5X-RAY DIFFRACTION4AA455 - 529455 - 529
6X-RAY DIFFRACTION5BB4 - 994 - 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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