[English] 日本語
Yorodumi
- PDB-1iwp: Glycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1iwp
TitleGlycerol Dehydratase-cyanocobalamin Complex of Klebsiella pneumoniae
Components(Glycerol Dehydratase ...) x 3
KeywordsLYASE / B12 / GLYCEROL DEHYDRATASE / KLEBSIELLA PNEUMONIAE / COBALAMIN / RADICAL CATALYSIS
Function / homology
Function and homology information


glycerol dehydratase / glycerol dehydratase activity / propanediol dehydratase / propanediol dehydratase activity / cobalamin binding
Similarity search - Function
Propanediol/glycerol dehydratase, small subunit / Diol/glycerol dehydratase, large subunit / Hypothetical Protein Yqey; Chain: A; domain1 / Diol/glycerol dehydratase, large subunit / Propanediol/glycerol dehydratase, small subunit / Propanediol/glycerol dehydratase, medium subunit / Propanediol/glycerol dehydratase, small subunit superfamily / Diol/glycerol dehydratase, large subunit superfamily / Dehydratase large subunit / Dehydratase small subunit ...Propanediol/glycerol dehydratase, small subunit / Diol/glycerol dehydratase, large subunit / Hypothetical Protein Yqey; Chain: A; domain1 / Diol/glycerol dehydratase, large subunit / Propanediol/glycerol dehydratase, small subunit / Propanediol/glycerol dehydratase, medium subunit / Propanediol/glycerol dehydratase, small subunit superfamily / Diol/glycerol dehydratase, large subunit superfamily / Dehydratase large subunit / Dehydratase small subunit / Diol/glycerol dehydratase/dehydratase reactivating factor / Dehydratase medium subunit / B12-dependent dehydatase associated subunit / B12-dependent dehydratases, beta subunit / Cobalamin (vitamin B12)-dependent enzyme, catalytic / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COBALAMIN / : / S-1,2-PROPANEDIOL / Glycerol dehydrase beta subunit / Glycerol dehydrase gamma subunit / Glycerol dehydrase alpha subunit
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYamanishi, M. / Yunoki, M. / Tobimatsu, T. / Toraya, T.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: The crystal structure of coenzyme B12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol.
Authors: Yamanishi, M. / Yunoki, M. / Tobimatsu, T. / Sato, H. / Matsui, J. / Dokiya, A. / Iuchi, Y. / Oe, K. / Suto, K. / Shibata, N. / Morimoto, Y. / Yasuoka, N. / Toraya, T.
History
DepositionMay 28, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.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_asym_id / _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_asym_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_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: Glycerol Dehydratase Alpha subunit
B: Glycerol Dehydratase Beta subunit
G: Glycerol Dehydratase Gamma subunit
L: Glycerol Dehydratase Alpha subunit
E: Glycerol Dehydratase Beta subunit
M: Glycerol Dehydratase Gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,34812
Polymers196,4576
Non-polymers2,8916
Water15,871881
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26360 Å2
ΔGint-130 kcal/mol
Surface area52250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.380, 108.223, 113.141
Angle α, β, γ (deg.)90.00, 96.75, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Glycerol Dehydratase ... , 3 types, 6 molecules ALBEGM

#1: Protein Glycerol Dehydratase Alpha subunit / glycerol dehydrase alpha subunit


Mass: 60714.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 25955 / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / References: UniProt: Q59476, glycerol dehydratase
#2: Protein Glycerol Dehydratase Beta subunit / glycerol dehydrase beta subunit


Mass: 21385.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 25955 / Plasmid: pUSI2E, pET19b / Production host: Escherichia coli (E. coli) / References: UniProt: O08505, glycerol dehydratase
#3: Protein Glycerol Dehydratase Gamma subunit / glycerol dehydrase gamma subunit


Mass: 16128.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 25955 / Plasmid: pUSI2E / Production host: Escherichia coli (E. coli) / References: UniProt: Q59475, glycerol dehydratase

-
Non-polymers , 4 types, 887 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 881 / 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: 3.03 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion (sandwitch drop) / pH: 8
Details: 20mM Tris-HCl, 15% PEG6000, 0.2M Na2SO4, pH 8.0, VAPOR DIFFUSION (Sandwitch Drop), temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: sandwich-drop vapor diffusion / Details: Shibata, N., (1999) Structure, 7, 997.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG60001reservoir
20.24 Mammonium sulfate1reservoir
320 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.816 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jan 19, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.816 Å / Relative weight: 1
ReflectionResolution: 2→45.175 Å / Num. all: 130797 / Num. obs: 130797 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.087 / Rsym value: 0.132 / Net I/σ(I): 4.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / % possible all: 97.6
Reflection
*PLUS
Num. obs: 130635 / Num. measured all: 958394 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.38

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB id, 1DIO

1dio


Resolution: 2.1→45 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 11285 10 %random
Rwork0.209 ---
all-113515 --
obs-113453 99.9 %-
Displacement parametersBiso mean: 28.73 Å2
Baniso -1Baniso -2Baniso -3
1--9.671 Å20 Å22.061 Å2
2---3.285 Å20 Å2
3---12.956 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13556 0 194 881 14631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0063
X-RAY DIFFRACTIONc_angle_deg1.32008
X-RAY DIFFRACTIONc_dihedral_angle_d21.48409
X-RAY DIFFRACTIONc_improper_angle_d0.88607
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3036 1151 10.16 %
Rwork0.2606 10179 -
Refinement
*PLUS
Lowest resolution: 45 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.48409
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88607
LS refinement shell
*PLUS
Rfactor Rfree: 0.3036 / Rfactor Rwork: 0.2606

+
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