[English] 日本語
Yorodumi
- PDB-2b5w: Crystal structure of D38C glucose dehydrogenase mutant from Halof... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b5w
TitleCrystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei
Componentsglucose dehydrogenase
KeywordsOXIDOREDUCTASE / Nucleotide binding motif
Function / homology
Function and homology information


non-phosphorylated glucose catabolic process / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)+] activity / D-glucose binding / NADP+ binding / NAD+ binding / protein homodimerization activity / zinc ion binding / identical protein binding
Similarity search - Function
Glucose 1-dehydrogenase, archaea / Glucose dehydrogenase, C-terminal / Glucose dehydrogenase C-terminus / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Glucose 1-dehydrogenase, archaea / Glucose dehydrogenase, C-terminal / Glucose dehydrogenase C-terminus / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glucose 1-dehydrogenase
Similarity search - Component
Biological speciesHaloferax mediterranei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBritton, K.L. / Baker, P.J. / Fisher, M. / Ruzheinikov, S. / Gilmour, D.J. / Bonete, M.-J. / Ferrer, J. / Pire, C. / Esclapez, J. / Rice, D.W.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei.
Authors: Britton, K.L. / Baker, P.J. / Fisher, M. / Ruzheinikov, S. / Gilmour, D.J. / Bonete, M.-J. / Ferrer, J. / Pire, C. / Esclapez, J. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Analysis of Glucose Dehydrogenase from Haloferax Mediterranei
Authors: Ferrer, J. / Fisher, M. / Burke, J. / Sedelnikova, S.E. / Baker, P.J. / Gilmour, D.J. / Bonete, M.-J. / Pire, C. / Esclapez, J. / Rice, D.W.
History
DepositionSep 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: glucose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4649
Polymers39,2711
Non-polymers1,1938
Water12,160675
1
A: glucose dehydrogenase
hetero molecules

A: glucose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,92818
Polymers78,5422
Non-polymers2,38716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area10140 Å2
ΔGint-96 kcal/mol
Surface area27370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.534, 109.255, 151.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1552-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein glucose dehydrogenase


Mass: 39270.781 Da / Num. of mol.: 1 / Mutation: C38D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax mediterranei (archaea) / Gene: gdh / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q977U7, glucose 1-dehydrogenase [NAD(P)+]

-
Non-polymers , 5 types, 683 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, temperature 290K, Vapor diffusion, hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 290 KK

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 16, 2002 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 66155 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.85
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.69 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B5V

2b5v


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.374 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.072 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.186 3356 5.1 %RANDOM
Rwork0.154 ---
obs-62795 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.16 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 67 675 3509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212914
X-RAY DIFFRACTIONr_bond_other_d0.0020.022552
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.983984
X-RAY DIFFRACTIONr_angle_other_deg0.85435953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023286
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02567
X-RAY DIFFRACTIONr_nbd_refined0.230.2600
X-RAY DIFFRACTIONr_nbd_other0.2450.23076
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.215
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.98621799
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.13632913
X-RAY DIFFRACTIONr_scbond_it14.4221115
X-RAY DIFFRACTIONr_scangle_it16.68731071
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 252
Rwork0.233 4459

+
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