[English] 日本語
Yorodumi
- PDB-2ri6: Crystal Structure of S112A mutant of a C-C hydrolase, BphD from B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ri6
TitleCrystal Structure of S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400
Components2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
KeywordsHYDROLASE / C-C bond hydrolase / Aromatic hydrocarbons catabolism
Function / homology
Function and homology information


2-hydroxy-6-oxonona-2,4-dienedioate hydrolase activity / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase / 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity / catabolic process
Similarity search - Function
2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, BphD / : / Alpha/beta hydrolase family / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.68 Å
AuthorsBhowmik, S. / Bolin, J.T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The tautomeric half-reaction of BphD, a C-C bond hydrolase. Kinetic and structural evidence supporting a key role for histidine 265 of the catalytic triad.
Authors: Horsman, G.P. / Bhowmik, S. / Seah, S.Y. / Kumar, P. / Bolin, J.T. / Eltis, L.D.
History
DepositionOct 10, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionNov 6, 2007ID: 2PU6
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9764
Polymers31,7491
Non-polymers2273
Water2,594144
1
A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules

A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules

A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules

A: 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,90516
Polymers126,9974
Non-polymers90812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.293, 117.293, 87.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase


Mass: 31749.268 Da / Num. of mol.: 1 / Mutation: S112A / Source method: isolated from a natural source / Source: (natural) Burkholderia xenovorans (bacteria) / Strain: LB400 / References: UniProt: P47229, EC: 3.7.1.-
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.9 M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 34855 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.3 % / Rsym value: 12.6 / Net I/σ(I): 18.6
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 8.1 / Num. unique all: 3424 / Rsym value: 27.1 / % possible all: 99.3

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.68→44.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.825 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1752 5 %RANDOM
Rwork0.175 ---
obs0.176 34845 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.173 Å
Refinement stepCycle: LAST / Resolution: 1.68→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 15 144 2398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222345
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9553182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4845296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.76723.964111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1941514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021819
X-RAY DIFFRACTIONr_nbd_refined0.20.21143
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2121
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.216
X-RAY DIFFRACTIONr_mcbond_it3.91921420
X-RAY DIFFRACTIONr_mcangle_it5.71532275
X-RAY DIFFRACTIONr_scbond_it9.1532968
X-RAY DIFFRACTIONr_scangle_it11.4283900
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 120 -
Rwork0.202 2385 -
all-2505 -
obs--98.82 %

+
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