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- PDB-1pgp: CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRA... -

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Basic information

Entry
Database: PDB / ID: 1pgp
TitleCRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM
Components6-PHOSPHOGLUCONATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (CHOH(D)-NADP+(A))
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / D-gluconate metabolic process / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt / NADP binding / cytoplasm
Similarity search - Function
6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase ...6-Phosphogluconate Dehydrogenase, domain 3 / 6-phosphogluconate-binding site / 6-phosphogluconate dehydrogenase signature. / 6-phosphogluconate dehydrogenase, decarboxylating / 6-phosphogluconate dehydrogenase, C-terminal / 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, C-terminal domain / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-PHOSPHOGLUCONIC ACID / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsAdams, M.J. / Phillips, C. / Gover, S. / Naylor, C.E.
Citation
Journal: Structure / Year: 1994
Title: Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism.
Authors: Adams, M.J. / Ellis, G.H. / Gover, S. / Naylor, C.E. / Phillips, C.
#1: Journal: To be Published
Title: The Structure of 6-Phosphogluconate Dehydrogenase Refined at 2 Angstroms Resolution
Authors: Phillips, C. / Gover, S. / Adams, M.J.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: The Structure of 6-Phosphogluconate Dehydrogenase Refined at 2.5 Angstroms Resolution
Authors: Adams, M.J. / Gover, S. / Leaback, R. / Phillips, C. / Somers, D.O'N.
History
DepositionJul 18, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 6-PHOSPHOGLUCONATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2783
Polymers52,9061
Non-polymers3722
Water7,170398
1
A: 6-PHOSPHOGLUCONATE DEHYDROGENASE
hetero molecules

A: 6-PHOSPHOGLUCONATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5566
Polymers105,8112
Non-polymers7444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12590 Å2
ΔGint-124 kcal/mol
Surface area33710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.740, 148.400, 102.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO 67
2: LYS 459 - PRO 460 OMEGA = 142.91 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Components on special symmetry positions
IDModelComponents
11A-1227-

HOH

21A-1590-

HOH

31A-1592-

HOH

41A-1593-

HOH

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Components

#1: Protein 6-PHOSPHOGLUCONATE DEHYDROGENASE


Mass: 52905.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep)
References: UniProt: P00349, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Sugar ChemComp-6PG / 6-PHOSPHOGLUCONIC ACID


Type: D-saccharide / Mass: 276.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O10P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE HET GROUP, 6-PHOSPHOGLUCONIC ACID, IS IONIZED AND CARRIES A NET -- CHARGE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/ml6-phosphogluconate dehydrogenase1drop
230 mM6-phosphogluconate1drop
340 %satammonium sulfate1drop
454 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 17989 / % possible obs: 92.8 % / Num. measured all: 44279 / Rmerge(I) obs: 0.0825

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.17 / Rfactor obs: 0.17 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 22 398 4074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg2.37
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: 20 Å / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.3
X-RAY DIFFRACTIONx_improper_angle_d1.3

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