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

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Basic information

Entry
Database: PDB / ID: 1pgq
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


D-gluconate metabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / 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
ADENOSINE-2'-MONOPHOSPHATE / 6-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / Resolution: 3.17 Å
AuthorsAdams, M.J. / Phillips, C. / Gover, S.
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 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 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)53,5415
Polymers52,9061
Non-polymers6354
Water7,584421
1
A: 6-PHOSPHOGLUCONATE DEHYDROGENASE
hetero molecules

A: 6-PHOSPHOGLUCONATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,08210
Polymers105,8112
Non-polymers1,2718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area13400 Å2
ΔGint-177 kcal/mol
Surface area33640 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

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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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-2AM / ADENOSINE-2'-MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE HET GROUP 2AM, 2'-ADENYLIC ACID, CARRIES A -- 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: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMammonium sulfate11
2potassium phosphate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.17 Å / Num. obs: 8942 / % possible obs: 92.2 % / Num. measured all: 29208 / Rmerge(I) obs: 0.063

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.169 / Rfactor obs: 0.169 / Highest resolution: 3.17 Å
Details: HET GROUP 2AM IS DESIGNATED 2'AMP IN THE JRNL REFERENCE. ATOMIC TEMPERATURE FACTORS AND SOLVENT OCCUPANCY AND POSITIONS WERE TAKEN FROM THE NATIVE STRUCTURE AT AN INTERMEDIATE STAGE OF ...Details: HET GROUP 2AM IS DESIGNATED 2'AMP IN THE JRNL REFERENCE. ATOMIC TEMPERATURE FACTORS AND SOLVENT OCCUPANCY AND POSITIONS WERE TAKEN FROM THE NATIVE STRUCTURE AT AN INTERMEDIATE STAGE OF REFINEMENT AND NOT REFINED. SOLVENT MOLECULES ARE ASSOCIATED WITH THE SAME MOLECULE AS THEIR CLOSEST OXYGEN OR NITROGEN NEIGHBOR; THIS BEST PRESERVES NETWORKS, BUT IN SOME INSTANCES HAS RESULTED IN THE NEAREST PROTEIN RESIDUE BEING THAT IN A SYMMETRY-RELATED MOLECULE. FOR SOME SOLVENT MOLECULES, THE DISTANCE TO THE CLOSEST OXYGEN OR NITROGEN NEIGHBOR IS MORE THAN 4 ANGSTROMS; THIS IS BECAUSE POORLY DEFINED SOLVENT SITES WERE OMITTED FROM NATIVE STRUCTURE REFINEMENT. THE CRITERIA APPLIED ARE DESCRIBED IN THE JRNL REFERENCE AND IN REFERENCE 1.
Refinement stepCycle: LAST / Highest resolution: 3.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3654 0 38 421 4113
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.043
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_deg2.75
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
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_deg1.73

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