[English] 日本語
Yorodumi
- PDB-1i7o: CRYSTAL STRUCTURE OF HPCE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i7o
TitleCRYSTAL STRUCTURE OF HPCE
Components4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
KeywordsISOMERASE / LYASE / bifunctional enzyme / decarboxylase
Function / homology
Function and homology information


5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase / 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase activity / 5-carboxymethyl-2-hydroxymuconate Delta-isomerase / 4-hydroxyphenylacetate catabolic process / 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity / metal ion binding
Similarity search - Function
4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit / 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase C-terminal / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Homoprotocatechuate catabolism bifunctional isomerase/decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsTame, J.R.H. / Namba, K. / Dodson, E.J. / Roper, D.I.
CitationJournal: To be Published
Title: The crystal structure of HpcE, a multi-functional enzyme fold
Authors: Tame, J.R.H. / Namba, K. / Dodson, E.J. / Roper, D.I.
History
DepositionMar 10, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_conn.ptnr2_label_seq_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: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
B: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
C: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
D: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,7778
Polymers188,6174
Non-polymers1604
Water12,034668
1
A: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1942
Polymers47,1541
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1942
Polymers47,1541
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1942
Polymers47,1541
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1942
Polymers47,1541
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.084, 138.201, 103.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
4-HYDROXYPHENYLACETATE DEGRADATION BIFUNCTIONAL ISOMERASE/DECARBOXYLASE


Mass: 47154.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P37352, 5-carboxymethyl-2-hydroxymuconate Delta-isomerase, 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: monomethylether PEG2000, calcium chloride, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop contains protein and reservoir solution in a 1:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
215 %mPEG20001reservoir
3200 mM1reservoirCaCl2
450 mMTris-HCl1reservoir

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. all: 198751 / Num. obs: 196319 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.6
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.2 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 91.2 Å / % possible obs: 98.5 %
Reflection shell
*PLUS
% possible obs: 98.3 %

-
Processing

Software
NameClassification
MAR345data collection
DENZOdata reduction
MLPHAREphasing
REFMACrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.7→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 9927 5.1 %RANDOM
Rwork0.2513 ---
all0.2527 198751 --
obs0.2527 186392 98.8 %-
Displacement parametersBiso mean: 44.65 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12947 0 4 668 13619
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.021
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1091.5
X-RAY DIFFRACTIONp_mcangle_it1.8412
X-RAY DIFFRACTIONp_scbond_it2.7373
X-RAY DIFFRACTIONp_scangle_it4.2234.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 91.2 Å / Num. reflection obs: 186453 / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.2155
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8511.964

+
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