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- PDB-1pgj: X-RAY STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE FROM THE PROT... -

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Entry
Database: PDB / ID: 1pgj
TitleX-RAY STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE FROM THE PROTOZOAN PARASITE T. BRUCEI
Components6-PHOSPHOGLUCONATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CHOH(D)-NADP+(B)
Function / homology
Function and homology information


phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / D-gluconate metabolic process / phosphogluconate dehydrogenase (decarboxylating) activity / glycosome / pentose-phosphate shunt / ciliary plasm / 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-phosphogluconate dehydrogenase, decarboxylating
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsDohnalek, J. / Phillips, C. / Gover, S. / Barrett, M.P. / Adams, M.J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: A 2.8 A resolution structure of 6-phosphogluconate dehydrogenase from the protozoan parasite Trypanosoma brucei: comparison with the sheep enzyme accounts for differences in activity with ...Title: A 2.8 A resolution structure of 6-phosphogluconate dehydrogenase from the protozoan parasite Trypanosoma brucei: comparison with the sheep enzyme accounts for differences in activity with coenzyme and substrate analogues.
Authors: Phillips, C. / Dohnalek, J. / Gover, S. / Barrett, M.P. / Adams, M.J.
#1: Journal: Protein Expr.Purif. / Year: 1994
Title: Overexpression in Escherichia Coli and Purification of the 6-Phosphogluconate Dehydrogenase of Trypanosoma Brucei
Authors: Barrett, M.P. / Phillips, C. / Adams, M.J. / Le Page, R.W.
#2: 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.
#3: Journal: Structure / Year: 1994
Title: Erratum. 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.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Study of 6-Phosphogluconate Dehydrogenase from Trypanosoma Brucei
Authors: Phillips, C. / Barrett, M.P. / Gover, S. / Le Page, R.W. / Adams, M.J.
History
DepositionMar 16, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 1.5Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / 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
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-PHOSPHOGLUCONATE DEHYDROGENASE
B: 6-PHOSPHOGLUCONATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5676
Polymers104,1832
Non-polymers3844
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-143 kcal/mol
Surface area32480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.130, 135.130, 116.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-544-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.48179, -0.85365, -0.19789), (-0.85296, -0.50861, 0.11737), (-0.20084, 0.11225, -0.97317)
Vector: 11.74451, -9.59825, 128.33745)

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Components

#1: Protein 6-PHOSPHOGLUCONATE DEHYDROGENASE / 6PGDH / 6-PGDH


Mass: 52091.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: BRUCEI / Cell line: BL21 / Gene: T. BRUCEI GND / Variant: TRUC427 / Plasmid: PT7GND / Species (production host): Escherichia coli / Gene (production host): T. BRUCEI GND / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P31072, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.5 %
Description: DATA COLLECTED BY OSCILLATION METHOD IN STEPS OF 1 DEGREE IN PHI. R SYM GIVEN IS FOR I > 4 SIG(I).
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALLISED FROM HANGING DROP WHICH ALSO CONTAINED 50MM POTASSIUM PHOSPHATE, 5MM DTT AND 30% SATURATED AMMONIUM SULPHATE, PH 7.0. THE WELL SOLUTION WAS 45% SATURATED AMMONIUM SULPHATE., ...Details: CRYSTALLISED FROM HANGING DROP WHICH ALSO CONTAINED 50MM POTASSIUM PHOSPHATE, 5MM DTT AND 30% SATURATED AMMONIUM SULPHATE, PH 7.0. THE WELL SOLUTION WAS 45% SATURATED AMMONIUM SULPHATE., vapor diffusion - hanging drop
Crystal grow
*PLUS
Details: Barrett, M.P., (1994) Protein Expr. Purif., 5, 44.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1992 / Details: COLLIMATOR, DUAL SLITS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 29373 / % possible obs: 95.9 % / Redundancy: 7.2 % / Rsym value: 0.099 / Net I/σ(I): 17.9
Reflection
*PLUS
Observed criterion σ(I): 4 / Num. measured all: 212041 / Rmerge(I) obs: 0.099

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
SSMdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SHEEP DIMER - SEE PDB ENTRY 2PGD

2pgd


Resolution: 2.82→19.76 Å / Data cutoff low absF: 0
Isotropic thermal model: TARGET SIGMA FOR 1-2 B FA PAIRS (BOND), 1-3 PAIRS (ANGLE)
Cross valid method: SEE JRNL REFERENCE / σ(F): 0
Details: FOR DETAILS OF RESTRAINED RESIDUES AND PARAMETERS USED IN BULK SOLVENT MODELLING, SEE JRNL REFERENCE. COORDINATES GIVEN ARE THOSE AFTER A FINAL NON-PARTITIONED (I.E., ALL DATA) REFINEMENT ...Details: FOR DETAILS OF RESTRAINED RESIDUES AND PARAMETERS USED IN BULK SOLVENT MODELLING, SEE JRNL REFERENCE. COORDINATES GIVEN ARE THOSE AFTER A FINAL NON-PARTITIONED (I.E., ALL DATA) REFINEMENT CYCLE, FOR WHICH R = 0.188 AND BIN R = 0.267.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1436 4.9 %RANDOM
Rwork0.186 ---
obs0.186 29307 97.7 %-
Displacement parametersBiso mean: 26.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.82→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7302 0 20 129 7451
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.7
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_it2.891.5
X-RAY DIFFRACTIONx_mcangle_it4.492
X-RAY DIFFRACTIONx_scbond_it2.891.5
X-RAY DIFFRACTIONx_scangle_it4.492
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 2.14 Å2 / Rms dev position: 0.1 Å / Weight Biso : 2 / Weight position: 80
LS refinement shellResolution: 2.82→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.352 150 5.4 %
Rwork0.268 2611 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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