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- PDB-3gg9: CRYSTAL STRUCTURE OF putative D-3-phosphoglycerate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 3gg9
TitleCRYSTAL STRUCTURE OF putative D-3-phosphoglycerate dehydrogenase oxidoreductase from Ralstonia solanacearum
Componentsd-3-phosphoglycerate dehydrogenase oxidoreductase protein
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / DEHYDROGENASE / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


phosphoglycerate dehydrogenase / phosphoglycerate dehydrogenase activity / NAD binding
Similarity search - Function
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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative d-3-phosphoglycerate dehydrogenase oxidoreductase protein
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPatskovsky, Y. / Ramagopal, U. / Toro, R. / Morano, C. / Freeman, J. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Putative D-3-Phosphoglycerate Dehydrogenase from Ralstonia Solanacearum
Authors: Patskovsky, Y. / Ramagopal, U. / Toro, R. / Morano, C. / Freeman, J. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: d-3-phosphoglycerate dehydrogenase oxidoreductase protein
B: d-3-phosphoglycerate dehydrogenase oxidoreductase protein
C: d-3-phosphoglycerate dehydrogenase oxidoreductase protein
D: d-3-phosphoglycerate dehydrogenase oxidoreductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,72623
Polymers155,0464
Non-polymers1,68019
Water17,096949
1
A: d-3-phosphoglycerate dehydrogenase oxidoreductase protein
D: d-3-phosphoglycerate dehydrogenase oxidoreductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,69115
Polymers77,5232
Non-polymers1,16813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-162 kcal/mol
Surface area27420 Å2
MethodPISA
2
B: d-3-phosphoglycerate dehydrogenase oxidoreductase protein
C: d-3-phosphoglycerate dehydrogenase oxidoreductase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0358
Polymers77,5232
Non-polymers5126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-126 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.034, 97.625, 97.808
Angle α, β, γ (deg.)90.00, 114.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
Detailshomodimer

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Components

#1: Protein
d-3-phosphoglycerate dehydrogenase oxidoreductase protein


Mass: 38761.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: serA, RSc0016 / References: UniProt: Q8Y3G4, phosphoglycerate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 949 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE SEQUENCE IN THE PDB ENTRY DOES NOT MATCH THE PREDICTED PROTEIN SEQUENCE OF ...AUTHORS STATE THAT THE SEQUENCE IN THE PDB ENTRY DOES NOT MATCH THE PREDICTED PROTEIN SEQUENCE OF UNIPROT ENTRY Q8Y3G4 AND THOSE MISMATCHES HAVE TO BE LISTED AS CONFLICTS.

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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: 2.58 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100MM BIS-TRIS, 25% PEG3350, PH 5.5, 200MM AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 124032 / % possible obs: 96.2 % / Observed criterion σ(I): -5 / Redundancy: 4.9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1 / % possible all: 73.6

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.714 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26138 3603 3 %RANDOM
Rwork0.19913 ---
obs0.201 115411 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.661 Å2
Baniso -1Baniso -2Baniso -3
1--2.55 Å20 Å2-1.82 Å2
2--2.52 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10527 0 93 949 11569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211113
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.97315092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46851454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70723.127502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49151992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.99115117
X-RAY DIFFRACTIONr_chiral_restr0.0860.21732
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028323
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1660.35322
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.57520
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.51537
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.383
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.533
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.51227117
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.716311149
X-RAY DIFFRACTIONr_scbond_it5.82934441
X-RAY DIFFRACTIONr_scangle_it8.14753896
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2406 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.60.3
medium positional0.570
medium positional0.620
medium positional0.580
medium thermal8.262
medium thermal8.530
medium thermal10.550
medium thermal9.910
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 179 -
Rwork0.312 6261 -
obs--70.82 %

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