[English] 日本語
Yorodumi
- PDB-9bke: STRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bke
TitleSTRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGENASE COMPONENT FROM ESCHERICHIA COLI MUTANT XS6 WITH AMP BOUND
Components4-hydroxyphenylacetate 3-monooxygenase oxygenase component
KeywordsOXIDOREDUCTASE / Flavin-dependent Hydroxylase
Function / homology
Function and homology information


4-hydroxyphenylacetate 3-monooxygenase activity / 4-hydroxyphenylacetate 3-monooxygenase / oxidoreductase activity, acting on the CH-CH group of donors / phenylacetate catabolic process / flavin adenine dinucleotide binding
Similarity search - Function
4-hydroxyphenylacetate 3-monooxygenase oxygenase component, gammaproteobacteria / 4-HPA 3-monooxygenase large component/Pyoverdin chromophore biosynthetic protein / HpaB/PvcC/4-BUDH / HpaB/PvcC/4-BUDH N-terminal / HpaB/PvcC/4-BUDH C-terminal / 4-hydroxyphenylacetate 3-hydroxylase C terminal / 4-hydroxyphenylacetate 3-hydroxylase N terminal / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: STRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGENASE COMPONENT FROM ESCHERICHIA COLI MUTANT XS6 WITH AMP BOUND
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionApr 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
B: 4-hydroxyphenylacetate 3-monooxygenase oxygenase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2314
Polymers119,5372
Non-polymers6942
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-56 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.233, 100.233, 335.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-951-

HOH

21B-971-

HOH

31B-975-

HOH

-
Components

#1: Protein 4-hydroxyphenylacetate 3-monooxygenase oxygenase component / 4-hydroxyphenylacetate 3-monooxygenase / oxygenase component


Mass: 59768.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: hpaB, CR538_21835, DS732_04180, NCTC9045_04991, NCTC9117_05338
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2G8ZEZ1, 4-hydroxyphenylacetate 3-monooxygenase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 16% Polyethylene Glycol 8000, 0.08M Sodium Cacodylate pH 6.5 0.16M Magnesium Acetate tetrahydrate 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 180771 / % possible obs: 99.1 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 18.83
Reflection shellResolution: 1.96→1.99 Å / Rmerge(I) obs: 0.838 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1856

-
Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→39.74 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 3266 1.81 %
Rwork0.1833 --
obs0.1839 180771 76.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8163 0 46 804 9013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128406
X-RAY DIFFRACTIONf_angle_d1.30511400
X-RAY DIFFRACTIONf_dihedral_angle_d16.2223088
X-RAY DIFFRACTIONf_chiral_restr0.0611208
X-RAY DIFFRACTIONf_plane_restr0.0111481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.217390.23962005X-RAY DIFFRACTION20
1.98-2.010.2425450.22682463X-RAY DIFFRACTION24
2.01-2.040.2837580.23643026X-RAY DIFFRACTION30
2.04-2.080.2622590.22583703X-RAY DIFFRACTION37
2.08-2.120.2563800.24474490X-RAY DIFFRACTION44
2.12-2.160.25671030.23295449X-RAY DIFFRACTION54
2.16-2.20.31431180.2376174X-RAY DIFFRACTION61
2.2-2.250.24911190.22076629X-RAY DIFFRACTION65
2.25-2.30.23851240.21946993X-RAY DIFFRACTION69
2.3-2.360.24861430.20147528X-RAY DIFFRACTION74
2.36-2.420.21971630.20128339X-RAY DIFFRACTION82
2.42-2.50.23271720.19999523X-RAY DIFFRACTION93
2.5-2.580.26591770.194410004X-RAY DIFFRACTION98
2.58-2.670.22881920.197610108X-RAY DIFFRACTION100
2.67-2.770.22061910.188610164X-RAY DIFFRACTION100
2.77-2.90.23031870.191510114X-RAY DIFFRACTION100
2.9-3.050.23351820.184510123X-RAY DIFFRACTION100
3.05-3.250.23051890.183910158X-RAY DIFFRACTION100
3.25-3.50.18241820.173610103X-RAY DIFFRACTION100
3.5-3.850.20861940.157610166X-RAY DIFFRACTION100
3.85-4.40.17311810.147610085X-RAY DIFFRACTION99
4.4-5.540.17561890.156710119X-RAY DIFFRACTION100
5.55-39.740.17831790.184210039X-RAY DIFFRACTION99

+
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