[English] 日本語
Yorodumi
- PDB-1e7y: ACTIVE SITE MUTANT (D177->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e7y
TitleACTIVE SITE MUTANT (D177->N) OF GLUCOSE 6-PHOSPHATE DEHYDROGENASE FROM LEUCONOSTOC MESENTEROIDES COMPLEXED WITH SUBSTRATE AND NADPH
ComponentsGLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (CHOH(D) - NAD(P)) / GLUCOSE METABOLISM
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase [NAD(P)+] / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt, oxidative branch / glucose metabolic process / NADP binding / cytosol
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 speciesLEUCONOSTOC MESENTEROIDES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsAdams, M.J. / Cosgrove, M.S. / Gover, S.
Citation
Journal: Biochemistry / Year: 2000
Title: An Examination of the Role of Asp-177 in the His-Asp Catalytic Dyad of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase: X-Ray Structure and Ph Dependence of Kinetic Parameters of ...Title: An Examination of the Role of Asp-177 in the His-Asp Catalytic Dyad of Leuconostoc Mesenteroides Glucose 6-Phosphate Dehydrogenase: X-Ray Structure and Ph Dependence of Kinetic Parameters of the D177N Mutant Enzyme
Authors: Cosgrove, M.S. / Gover, S. / Naylor, C.E. / Vandeputte-Rutten, L. / Adams, M.J. / Levy, H.R.
#1: Journal: Biochemistry / Year: 1998
Title: On the Mechanism of the Reaction Catalysed by Glucose 6-Phosphate Dehydrogenase
Authors: Cosgrove, M.S. / Naylor, C. / Paludin, S. / Adams, M.J. / Levy, H.R.
#2: Journal: Structure / Year: 1994
Title: The Three-Dimensional Structure of Glucose 6-Phosphate Dehydrogenase from Leuconostoc Mesenteroides Refined at 2 Angstroms Resolution
Authors: Rowland, P. / Basak, A.K. / Gover, S. / Levy, H.R. / Adams, M.J.
History
DepositionSep 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
Revision 1.5May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.6May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.7Jul 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.8May 1, 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
Remark 650 HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO 2.0A L. MESENTEROIDES ... HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO 2.0A L. MESENTEROIDES STRUCTURE, 1DPG. HELIX_ID: A,BEND AT K21 IS CONSEQUENCE OF CONSERVED P24. HELIX_ID: B,THE LAST TURN IS 3_10 (CLASS 5). HELIX_ID: C,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: D,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: F,THE FIRST TURN IS 3_10 (CLASS 5). HELIX_ID: H,G231 BRIDGES H & I' SO IS NOT HELICAL. HELIX_ID: I',PART OF HELIX I IN 1DPG. RESIDUES 235-239 DISTORTED BY SIDECHAIN INTERACTION OF N239 WITH D235.
Remark 700 SHEET DETERMINATION METHOD: INITIAL AND TERMINAL RESIDUES ARE AS DEFINED BY PROCHECK. REGISTRATION ... SHEET DETERMINATION METHOD: INITIAL AND TERMINAL RESIDUES ARE AS DEFINED BY PROCHECK. REGISTRATION IS AS GIVEN BY HYDROGEN BONDS AND IN THE CASE OF SHEET COE INVOLVES RESIDUES THAT IMMEDIATELY PRECEDE EACH SHEET ELEMENT. THIS IS DONE TO PRESERVE OBSERVED CONSISTENCY WITH NATIVE STRUCTURE 1DPG.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4144
Polymers54,3691
Non-polymers1,0463
Water2,360131
1
A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules

A: GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8298
Polymers108,7372
Non-polymers2,0916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5440 Å2
ΔGint-47.7 kcal/mol
Surface area45510 Å2
MethodPQS
Unit cell
Length a, b, c (Å)129.000, 44.000, 91.100
Angle α, β, γ (deg.)90.00, 105.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2047-

HOH

DetailsBIOMOLECULE DIMERIC

-
Components

#1: Protein GLUCOSE 6-PHOSPHATE 1-DEHYDROGENASE / G6PD


Mass: 54368.660 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEUCONOSTOC MESENTEROIDES (bacteria)
Description: SITE DIRECTED MUTAGENESIS OTHER_DETAILS: SITE DIRECTED MUTAGENESIS
Gene: PLMZ/D177NURCE 9 / Plasmid: PUC-19/ASP177ASNPLMZ / Gene (production host): PLMZ/D177N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SU294
References: UniProt: P11411, 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION ASP177ASN BETA-D-GLUCOSE 6-PHOSPHATE + NADP(+) = D-GLUCONO-DELTA- ...CHAIN A ENGINEERED MUTATION ASP177ASN BETA-D-GLUCOSE 6-PHOSPHATE + NADP(+) = D-GLUCONO-DELTA-LACTONE 6-PHOSPHATE + NADPH.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 42.2 %
Description: MOLECULE LOCATED BY DIFFERENCE FOURIER AND RIGID-BODY REFINEMENT
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. IN THE WELL BUFFER: 14% W/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.5 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 15MG/ML, WITH 2.3MM GLUCOSE 6- ...Details: HANGING DROP VAPOUR DIFFUSION, 2+2 MICROLITER DROPS. IN THE WELL BUFFER: 14% W/V PEG 400 IN 0.1M HEPES-NAOH, PH 7.5 WITH 0.2M CALCIUM CHLORIDE. THE PROTEIN AT 15MG/ML, WITH 2.3MM GLUCOSE 6-PHOSPHATE AND 0.6MM NADPH.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlenzyme1drop
20.1 MTris-HCl1drop
329 mMNAD+1drop
420 %(v/v)PEG4001reservoir
50.1 MHEPES/NaOH1reservoir
60.2 M1reservoirCaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1998 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→22.9 Å / Num. obs: 16723 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rsym value: 0.106 / Net I/σ(I): 9
Reflection shellResolution: 2.48→2.59 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.46 / % possible all: 82.1
Reflection
*PLUS
Num. measured all: 38083 / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 82.1 % / Rmerge(I) obs: 0.46

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED COORDINATES OF APO-ENZYME IN THE SAME SPACEGROUP

Resolution: 2.48→22.9 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 0 / Details: BULK SOLVENT WAS MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 797 4.7 %RANDOM, USING XPLOR
Rwork0.205 ---
obs0.205 16723 93.6 %-
Displacement parametersBiso mean: 30.1 Å2
Refine analyzeLuzzati d res low obs: 22.9 Å / Luzzati sigma a obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.48→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 44 131 4015
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.29
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.97
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.841.5
X-RAY DIFFRACTIONx_mcangle_it5.352
X-RAY DIFFRACTIONx_scbond_it3.841.5
X-RAY DIFFRACTIONx_scangle_it5.352
LS refinement shellResolution: 2.48→2.59 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.428 97 5.3 %
Rwork0.353 1817 -
obs--82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3BG6.PARBG6.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 15926
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.97
LS refinement shell
*PLUS
Num. reflection Rwork: 1720

+
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://pdbjlvh1.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