[English] 日本語
Yorodumi
- PDB-5aq1: Trypanosoma cruzi Glucose-6-phosphate Dehydrogenase in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aq1
TitleTrypanosoma cruzi Glucose-6-phosphate Dehydrogenase in complex with G6P and NADPH
ComponentsGLUCOSE-6-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / PENTOSE PHOSPHATE PATHWAY / REDOX BALANCE / CHAGAS DISEASE / G6PD / G6PDH.
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / NADP binding
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal 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
6-O-phosphono-beta-D-glucopyranose / Chem-NDP / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMercaldi, G.F. / Dawson, A. / Hunter, W.N. / Cordeiro, A.T.
CitationJournal: FEBS Lett. / Year: 2016
Title: The Structure of a Trypanosoma Cruzi Glucose-6-Phosphate Dehydrogenase Reveals Differences from the Mammalian Enzyme.
Authors: Mercaldi, G.F. / Dawson, A. / Hunter, W.N. / Cordeiro, A.T.
History
DepositionSep 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
B: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
C: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,8789
Polymers172,8613
Non-polymers3,0176
Water4,558253
1
B: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
C: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules

B: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
C: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,50412
Polymers230,4824
Non-polymers4,0228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area15460 Å2
ΔGint-89.5 kcal/mol
Surface area94800 Å2
MethodPQS
2
A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules

A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules

A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules

A: GLUCOSE-6-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,50412
Polymers230,4824
Non-polymers4,0228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_665-y+3/2,-x+3/2,-z+1/21
crystal symmetry operation10_675-x+1,-y+2,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
Buried area15440 Å2
ΔGint-74.7 kcal/mol
Surface area94120 Å2
MethodPQS
Unit cell
Length a, b, c (Å)154.946, 154.946, 348.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein GLUCOSE-6-PHOSPHATE DEHYDROGENASE


Mass: 57620.449 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 58-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: CL BRENER / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4E0B2, glucose-6-phosphate dehydrogenase (NADP+)
#2: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTRUNCATED CONSTRUCT WITH 57 AMINOACIDS IN N TERMINUS AND 10 AMINOACIDS IN C TERMINUS REMOVED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.35 % / Description: NONE
Crystal growDetails: PROTEIN: 2UL TCG6PD 10MG/ML, 5MM G6P, 2 MM NADPH; BUFFER: 20 MM TRIS PH 8.0 WITH 0.2 M NACL AND 5 MM ME PRECIPITANT: 1 UL JEFFAMINE ED-2003 PH 7.0 30%, 0.1 M HEPES PH 7.0;

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 2.65→49.13 Å / Num. obs: 58510 / % possible obs: 95.4 % / Observed criterion σ(I): 2.5 / Redundancy: 8.7 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.5 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E9I

4e9i
PDB Unreleased entry


Resolution: 2.65→141.57 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 20.601 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.694 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22553 2941 5 %RANDOM
Rwork0.19991 ---
obs0.20118 55569 94.73 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.96 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.65→141.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11571 0 192 253 12016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01912018
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211475
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.98516290
X-RAY DIFFRACTIONr_angle_other_deg0.808326355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53251449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9323.158570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.113152064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.07515117
X-RAY DIFFRACTIONr_chiral_restr0.0560.21800
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02113422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022829
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5442.5315805
X-RAY DIFFRACTIONr_mcbond_other1.5442.535804
X-RAY DIFFRACTIONr_mcangle_it2.7253.7897251
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8042.8196212
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 223 -
Rwork0.311 4141 -
obs--96.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78370.4186-0.07991.2756-0.07520.6584-0.01640.037-0.2146-0.1162-0.0184-0.10570.25880.02850.03470.13680.03530.01810.0198-0.00070.200276.09122.5875.311
20.709-0.50510.13231.4416-0.15960.518-0.0232-0.06230.17810.15060.0314-0.1294-0.0925-0.0092-0.00820.1462-0.033400.0862-0.00810.263476.261109.68124.929
31.1693-0.4256-0.20581.0040.09120.8985-0.05360.05570.0927-0.02280.0448-0.32890.00290.36860.00870.15-0.0411-0.00030.223-0.0130.3341109.97175.249101.35
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A62 - 545
2X-RAY DIFFRACTION2B62 - 545
3X-RAY DIFFRACTION3C62 - 545

+
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