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- PDB-1gdh: CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT... -

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Basic information

Entry
Database: PDB / ID: 1gdh
TitleCRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION
ComponentsD-GLYCERATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(CHOH (D)-NAD(P)+ (A))
Function / homology
Function and homology information


glycerate dehydrogenase / glycerate dehydrogenase activity / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / 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 / 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 ...D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / 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 / 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
Glycerate dehydrogenase
Similarity search - Component
Biological speciesHyphomicrobium methylovorum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsGoldberg, J.D. / Yoshida, T. / Brick, P.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution.
Authors: Goldberg, J.D. / Yoshida, T. / Brick, P.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Preliminary Diffraction Studies of Hydroxypyruvate Reductase (D-Glycerate Dehydrogenase) from Hyphomicrobium Methylovorum
Authors: Goldberg, J.D. / Brick, P. / Yoshida, T. / Mitsunaga, T. / Oshiro, T. / Shimao, M. / Izumi, Y.
History
DepositionSep 22, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-GLYCERATE DEHYDROGENASE
B: D-GLYCERATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0614
Polymers69,8692
Non-polymers1922
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-54 kcal/mol
Surface area24420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.410, 60.530, 66.290
Angle α, β, γ (deg.)102.30, 113.73, 102.73
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 270 / 2: CIS PROLINE - PRO B 270
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.35079, -0.49109, 0.79736), (-0.48281, -0.82442, -0.29535), (0.8024, -0.28136, -0.5263)
Vector: 17.05181, 72.93915, 15.54483)

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Components

#1: Protein D-GLYCERATE DEHYDROGENASE


Mass: 34934.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomicrobium methylovorum (bacteria) / References: UniProt: P36234, glycerate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Goldberg, J.D., (1992) J.Mol.Biol., 225, 909.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMpotassium phosphate1drop
20.1 mMdithiothreitol1drop
318 mg/mlprotein1drop
445 %satammonium sulfate1drop
545 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 24903 / % possible obs: 80.8 % / Num. measured all: 41961 / Rmerge(I) obs: 0.048

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.189 / Rfactor obs: 0.189 / Highest resolution: 2.4 Å
Details: ONLY PARTIAL DNA SEQUENCE INFORMATION IS AVAILABLE. THE DNA SEQUENCE CORRESPONDING TO THE 130 N-TERMINAL RESIDUES IS KNOWN. FOR THE REMAINDER OF THE POLYPEPTIDE, SIDE-CHAIN IDENTITIES HAVE ...Details: ONLY PARTIAL DNA SEQUENCE INFORMATION IS AVAILABLE. THE DNA SEQUENCE CORRESPONDING TO THE 130 N-TERMINAL RESIDUES IS KNOWN. FOR THE REMAINDER OF THE POLYPEPTIDE, SIDE-CHAIN IDENTITIES HAVE BEEN INTERPRETED DIRECTLY FROM ELECTRON DENSITY MAPS. THE POSSIBILITY OF THERE BEING ADDITIONAL RESIDUES AT THE C-TERMINUS IS NOT DISCOUNTED.
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4829 0 10 197 5036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 24553 / Rfactor obs: 0.194 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.57

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