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- PDB-1cer: DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR ... -

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Basic information

Entry
Database: PDB / ID: 1cer
TitleDETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION
ComponentsHOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (ALDEHYDE(D)-NAD(A)) / GLYCOLYSIS / OXIDOREDUCTASE / NAD
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytoplasm
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsTanner, J.J. / Hecht, R.M. / Krause, K.L.
Citation
Journal: Biochemistry / Year: 1996
Title: Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticus D-glyceraldehyde-3-phosphate dehydrogenase at 25 Angstroms Resolution.
Authors: Tanner, J.J. / Hecht, R.M. / Krause, K.L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Preliminary Crystallographic Analysis of Glyceraldehyde-3-Phosphate Dehydrogenase from the Extreme Thermophile Thermus Aquaticus
Authors: Tanner, J. / Hecht, R.M. / Pisegna, M. / Seth, D.M. / Krause, K.L.
History
DepositionNov 11, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: 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
O: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
P: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Q: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
R: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
A: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
B: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
C: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
D: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,83816
Polymers287,5308
Non-polymers5,3078
Water00
1
O: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
P: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Q: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
R: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4198
Polymers143,7654
Non-polymers2,6544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20440 Å2
ΔGint-135 kcal/mol
Surface area41770 Å2
MethodPISA
2
A: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
B: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
C: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
D: HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4198
Polymers143,7654
Non-polymers2,6544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20460 Å2
ΔGint-136 kcal/mol
Surface area41760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.770, 148.770, 149.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9965, 0.03559, 0.07567), (-0.02517, -0.9906, 0.13447), (0.07975, 0.13209, 0.98802)
Vector: 66.57403, 73.2293, -7.52999)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC SYMMETRY THAT GENERATES THE SECOND TETRAMER IN THE ASYMMETRIC UNIT. THIS APPROXIMATE TWO-FOLD ROTATION AROUND Z THAT GENERATES THE SECOND OF TWO TETRAMERS IN THE ASYMMETRIC UNIT. NOTE THAT THIS ENTRY CONTAINS ONLY ONE TETRAMER.

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Components

#1: Protein
HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / GAPDH


Mass: 35941.273 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: THERMUS AQUATICUS GAPDH / Plasmid: PBR322 / Gene (production host): THERMUS AQUATICUS GAPDH / Production host: Escherichia coli (E. coli) / Strain (production host): W3CG
References: UniProt: P00361, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal grow
*PLUS
pH: 8.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme1drop
250 mM1dropNaCl
30.5 mMbeta-mercaptoethanol1drop
40.5 mMEDTA1drop
51 mMNAD1drop
61.25 mMTris-HCl1drop
77.5 %isopropanol1drop
810-12 %PEG30001drop
90.05 MHEPES1drop
1015 %isopropanol1reservoir
1120-24 %PEG30001reservoir
120.1 MHEPES1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 15, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 81628 / % possible obs: 72 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.0565
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 267328 / Rmerge(I) obs: 0.0565
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 30 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.5→12 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.205 --
obs0.205 80657 72 %
Displacement parametersBiso mean: 28.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19874 0 352 0 20226
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.021
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_deg2.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.32
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.95
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it11
X-RAY DIFFRACTIONx_mcangle_it1.51.5
X-RAY DIFFRACTIONx_scbond_it1.51.5
X-RAY DIFFRACTIONx_scangle_it22
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.32
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.95

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