[English] 日本語
Yorodumi
- PDB-2eb6: Crystal structure of HpcG complexed with Mg ion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2eb6
TitleCrystal structure of HpcG complexed with Mg ion
Components2-oxo-hept-3-ene-1,7-dioate hydratase
KeywordsLYASE / hydratase
Function / homology
Function and homology information


2-oxo-hept-3-ene-1,7-dioate hydratase activity / 2-hydroxyhexa-2,4-dienoate hydratase activity / 2-oxo-3-hexenedioate decarboxylase / 4-oxalocrotonate decarboxylase activity / 2-oxopent-4-enoate hydratase / 2-oxopent-4-enoate hydratase activity / catabolic process / metal ion binding
Similarity search - Function
2-oxo-hepta-4-ene-1,7-dioic acid hydratase / : / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-keto-4-pentenoate hydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsIzumi, A. / Rea, D. / Adachi, T. / Unzai, S. / Park, S.Y. / Roper, D.I. / Tame, J.R.H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and Mechanism of HpcG, a Hydratase in the Homoprotocatechuate Degradation Pathway of Escherichia coli
Authors: Izumi, A. / Rea, D. / Adachi, T. / Unzai, S. / Park, S.Y. / Roper, D.I. / Tame, J.R.H.
History
DepositionFeb 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 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
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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-oxo-hept-3-ene-1,7-dioate hydratase
B: 2-oxo-hept-3-ene-1,7-dioate hydratase
C: 2-oxo-hept-3-ene-1,7-dioate hydratase
D: 2-oxo-hept-3-ene-1,7-dioate hydratase
E: 2-oxo-hept-3-ene-1,7-dioate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,87610
Polymers148,7545
Non-polymers1225
Water17,421967
1
A: 2-oxo-hept-3-ene-1,7-dioate hydratase
B: 2-oxo-hept-3-ene-1,7-dioate hydratase
C: 2-oxo-hept-3-ene-1,7-dioate hydratase
D: 2-oxo-hept-3-ene-1,7-dioate hydratase
E: 2-oxo-hept-3-ene-1,7-dioate hydratase
hetero molecules

A: 2-oxo-hept-3-ene-1,7-dioate hydratase
B: 2-oxo-hept-3-ene-1,7-dioate hydratase
C: 2-oxo-hept-3-ene-1,7-dioate hydratase
D: 2-oxo-hept-3-ene-1,7-dioate hydratase
E: 2-oxo-hept-3-ene-1,7-dioate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,75120
Polymers297,50810
Non-polymers24310
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area24200 Å2
ΔGint-178 kcal/mol
Surface area94550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)135.955, 135.955, 194.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11D-1076-

HOH

21D-1122-

HOH

-
Components

#1: Protein
2-oxo-hept-3-ene-1,7-dioate hydratase / 2-oxo-hept-4-ene-1 / 7-dioate hydratase


Mass: 29750.828 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: strain C / Gene: HPCG / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q46982, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 967 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 7% PEG 12000, 0.1M MES, 0.7M potassium thiocyanate, 7% PEG 550 MME, 10mM DTT, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 195362 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.261 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EB4(apo-HpcG)

2eb4


Resolution: 1.69→10 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.64 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 9816 5 %RANDOM
Rwork0.1944 ---
obs0.19532 184822 97.32 %-
all-195362 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.179 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.69→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10461 0 5 967 11433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210685
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.96114510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21151328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.93323.713509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48151778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg171590
X-RAY DIFFRACTIONr_chiral_restr0.0750.21614
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028228
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.25015
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27382
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.060.215
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.2143
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.269
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5851.56860
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.956210734
X-RAY DIFFRACTIONr_scbond_it1.35134318
X-RAY DIFFRACTIONr_scangle_it2.2064.53776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.692→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 691 -
Rwork0.227 12991 -
obs--95.5 %

+
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