[English] 日本語
Yorodumi
- PDB-1pgj: X-RAY STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE FROM THE PROT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


D-gluconate metabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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 / Sulfate


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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.

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more