[English] 日本語
Yorodumi
- PDB-4zu3: Halohydrin hydrogen-halide-lyases, HheB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zu3
TitleHalohydrin hydrogen-halide-lyases, HheB
ComponentsHalohydrin epoxidase B
KeywordsLYASE
Function / homology
Function and homology information


Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-hydroxypentanedinitrile / Halohydrin epoxidase B
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWatanabe, F. / Yu, F. / Ohtaki, A. / Yamanaka, Y. / Noguchi, K. / Yohda, M. / Odaka, M.
CitationJournal: Proteins / Year: 2015
Title: Crystal structures of halohydrin hydrogen-halide-lyases from Corynebacterium sp. N-1074
Authors: Watanabe, F. / Yu, F. / Ohtaki, A. / Yamanaka, Y. / Noguchi, K. / Yohda, M. / Odaka, M.
History
DepositionMay 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 2.0Feb 19, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / diffrn_source / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _citation.journal_id_CSD ..._atom_site.occupancy / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Nov 8, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Halohydrin epoxidase B
B: Halohydrin epoxidase B
C: Halohydrin epoxidase B
D: Halohydrin epoxidase B
E: Halohydrin epoxidase B
F: Halohydrin epoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,83215
Polymers151,9416
Non-polymers8919
Water15,421856
1
A: Halohydrin epoxidase B
B: Halohydrin epoxidase B
C: Halohydrin epoxidase B
D: Halohydrin epoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,94010
Polymers101,2944
Non-polymers6476
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13400 Å2
ΔGint-81 kcal/mol
Surface area29350 Å2
MethodPISA
2
E: Halohydrin epoxidase B
F: Halohydrin epoxidase B
hetero molecules

E: Halohydrin epoxidase B
F: Halohydrin epoxidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,78310
Polymers101,2944
Non-polymers4896
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x,-y,-z-11
Buried area13720 Å2
ΔGint-94 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.910, 215.640, 104.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-302-

MG

21A-463-

HOH

31E-456-

HOH

41F-443-

HOH

-
Components

#1: Protein
Halohydrin epoxidase B


Mass: 25323.432 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Gene: hheB / Plasmid: pSTT002 / Production host: ESCHERICHIA COLI / Strain (production host): JM109 / References: UniProt: Q46347
#2: Chemical
ChemComp-4SD / 3-hydroxypentanedinitrile


Mass: 110.114 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H6N2O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG 4000, magnesium chloride, calcium chloride, MES [2-(N-morpholino) ethanesulfonic acid] buffer

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 71131 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 33.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 8.7 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10-2152-000)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZD6

4zd6


Resolution: 2.2→47.013 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3583 5.06 %RANDOM
Rwork0.1627 ---
obs0.165 70879 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→47.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10588 0 62 856 11506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410869
X-RAY DIFFRACTIONf_angle_d0.66714747
X-RAY DIFFRACTIONf_dihedral_angle_d14.2286356
X-RAY DIFFRACTIONf_chiral_restr0.0471623
X-RAY DIFFRACTIONf_plane_restr0.0041936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1941-2.2230.33311370.26342408X-RAY DIFFRACTION93
2.223-2.25340.34911460.30292523X-RAY DIFFRACTION99
2.2534-2.28560.35271370.26562521X-RAY DIFFRACTION98
2.2856-2.31970.24181530.19832559X-RAY DIFFRACTION100
2.3197-2.3560.26441410.18082566X-RAY DIFFRACTION100
2.356-2.39460.24091430.17592573X-RAY DIFFRACTION100
2.3946-2.43590.24181180.17432605X-RAY DIFFRACTION100
2.4359-2.48020.22521320.16912590X-RAY DIFFRACTION100
2.4802-2.52790.25341380.17542579X-RAY DIFFRACTION100
2.5279-2.57950.21781260.16792580X-RAY DIFFRACTION100
2.5795-2.63560.26251300.16712606X-RAY DIFFRACTION100
2.6356-2.69690.2431430.17192598X-RAY DIFFRACTION100
2.6969-2.76430.20721280.17192575X-RAY DIFFRACTION100
2.7643-2.8390.22851440.17332591X-RAY DIFFRACTION100
2.839-2.92260.22611380.16732588X-RAY DIFFRACTION100
2.9226-3.01690.19291550.16452580X-RAY DIFFRACTION100
3.0169-3.12470.22831320.17442602X-RAY DIFFRACTION100
3.1247-3.24980.1941490.16472602X-RAY DIFFRACTION100
3.2498-3.39760.2161200.16932601X-RAY DIFFRACTION100
3.3976-3.57670.19721330.16032615X-RAY DIFFRACTION100
3.5767-3.80070.19821340.14542591X-RAY DIFFRACTION99
3.8007-4.0940.1651660.13332587X-RAY DIFFRACTION100
4.094-4.50570.13851420.12092648X-RAY DIFFRACTION100
4.5057-5.1570.1631220.11752656X-RAY DIFFRACTION100
5.157-6.49450.16811410.14982678X-RAY DIFFRACTION100
6.4945-47.02350.20831350.16682674X-RAY DIFFRACTION96

+
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