[English] 日本語
Yorodumi
- PDB-6b1b: STRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b1b
TitleSTRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGENASE COMPONENT FROM ESCHERICHIA COLI MUTANT XS6 (APO Enzyme)
Components4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
KeywordsOXIDOREDUCTASE / PROTEIN ENGINEERING: 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE / OXYGENASE COMPONENT / OXIDOREDUCTASE ACTIVE SITE LOOP MUTANT 7.2
Function / homology
Function and homology information


4-hydroxyphenylacetate 3-monooxygenase / oxidoreductase activity, acting on the CH-CH group of donors / phenylacetate catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / 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
trimethylamine oxide / 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 Å
AuthorsZhou, D. / Kandavelu, P. / Wang, B.C. / Yan, Y. / Rose, J.P.
CitationJournal: Sci Rep / Year: 2019
Title: Structural Insights into Catalytic Versatility of the Flavin-dependent Hydroxylase (HpaB) from Escherichia coli.
Authors: Shen, X. / Zhou, D. / Lin, Y. / Wang, J. / Gao, S. / Kandavelu, P. / Zhang, H. / Zhang, R. / Wang, B.C. / Rose, J. / Yuan, Q. / Yan, Y.
History
DepositionSep 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,13810
Polymers119,5372
Non-polymers6018
Water19,1141061
1
A: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
B: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
hetero molecules

A: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
B: 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,27520
Polymers239,0734
Non-polymers1,20216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area34430 Å2
ΔGint-218 kcal/mol
Surface area60310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.455, 100.455, 336.435
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
11A-1143-

HOH

21A-1161-

HOH

31A-1202-

HOH

41B-2523-

HOH

51B-2556-

HOH

-
Components

#1: Protein 4-hydroxyphenylacetate 3-monooxygenase, oxygenase subunit


Mass: 59768.348 Da / Num. of mol.: 2 / Mutation: F208S, A211D, Q212L. V213G, M214S, E216S, N217D
Source method: isolated from a genetically manipulated source
Details: Active site loop mutant 7.2
Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria)
Strain: B / BL21-DE3 / Gene: ECBD_3674 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140NG21
#2: Chemical
ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C3H9NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1061 / 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: 3.66 Å3/Da / Density % sol: 66.42 %
Description: Crystal is a clear colorless prism measuring 80 BY 50 BY 10 microns
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP VAPOR DIFFUSION AT 291K USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION AND A WELL SOLUTION CONTAINING 1.0 M SUCCINIC ACID, 0.1 M HEPES, AND 1% W/V ...Details: HANGING DROP VAPOR DIFFUSION AT 291K USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION AND A WELL SOLUTION CONTAINING 1.0 M SUCCINIC ACID, 0.1 M HEPES, AND 1% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000 AT PH 7.0. CRYOPROTECTANT WAS MADE BY ADDING 30 % (V/V) GLYCEROL TO THE PRECIPITANT COCKTAIL.
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 8, 2017 / Details: ROSENBAUM ROCK
RadiationMonochromator: SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.944→46.36 Å / Num. obs: 127481 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 17.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 29.736
Reflection shellResolution: 1.944→1.98 Å / Redundancy: 16.8 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 8.449 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000V0.714data reduction
SCALEPACKV0.714data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UM5

5um5
PDB Unreleased entry


Resolution: 1.944→44.53 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 14.86
RfactorNum. reflection% reflection
Rfree0.1661 1999 1.57 %
Rwork0.1516 --
obs0.1518 127312 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.944→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8129 0 40 1061 9230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078353
X-RAY DIFFRACTIONf_angle_d0.93911325
X-RAY DIFFRACTIONf_dihedral_angle_d4.5374961
X-RAY DIFFRACTIONf_chiral_restr0.0541195
X-RAY DIFFRACTIONf_plane_restr0.0061473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9437-1.99230.20581390.17488676X-RAY DIFFRACTION99
1.9923-2.04620.19561410.16388827X-RAY DIFFRACTION100
2.0462-2.10640.19471410.15458852X-RAY DIFFRACTION100
2.1064-2.17440.17391400.15218832X-RAY DIFFRACTION100
2.1744-2.25210.17521420.14748855X-RAY DIFFRACTION100
2.2521-2.34230.16361420.14658877X-RAY DIFFRACTION100
2.3423-2.44890.17881420.15128913X-RAY DIFFRACTION100
2.4489-2.5780.17161420.15878890X-RAY DIFFRACTION100
2.578-2.73950.16771420.15288902X-RAY DIFFRACTION100
2.7395-2.9510.15621420.15248963X-RAY DIFFRACTION100
2.951-3.24790.15371440.14518976X-RAY DIFFRACTION100
3.2479-3.71760.14531440.13839044X-RAY DIFFRACTION100
3.7176-4.6830.161460.13519150X-RAY DIFFRACTION100
4.683-44.54130.16671520.17499556X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4047-0.14490.21220.4601-0.11841.2511-0.04150.1849-0.0082-0.40610.03050.15090.36930.23810.0159-0.0960.1570.18120.2604-0.0410.013542.7489-3.200714.7319
20.5254-0.0328-0.07310.4279-0.07260.44890.00330.10610.04760.0003-0.0412-0.0316-0.02970.12030.02690.060.01060.01170.20490.02610.093737.265512.034313.4538
30.54070.3-0.19830.6719-0.40230.7230.01810.010.09350.0618-0.0809-0.0652-0.06780.29360.04760.0654-0.00680.00790.25390.02650.14447.360412.725224.1376
40.3192-0.30740.10740.7683-0.12240.5257-0.00620.045-0.0220.1070.01890.06560.08470.00350.00290.0770.00990.00680.0858-0.00550.082119.35810.939529.8882
50.7138-0.38960.45412.44540.82220.8631-0.08190.02670.1264-0.07490.0083-0.03330.01810.08540.05490.10160.02960.00680.08820.00540.066727.13-1.627234.5746
60.7002-0.2059-0.0810.58990.0260.4817-0.05460.09370.11510.0317-0.018-0.0487-0.2221-0.03160.01130.18250.0179-0.03590.0750.00960.09116.816940.617229.9261
70.3931-0.1378-0.00260.40070.27140.901-0.04620.06950.0298-0.0183-0.01390.0294-0.1259-0.22320.03020.06630.0376-0.0290.16450.00280.0882-10.682326.852116.2268
80.57230.31960.31130.63560.44380.87720.0074-0.045-0.09160.1005-0.05590.06330.0724-0.31690.03660.0651-0.00460.00280.22730.00250.1373-17.877518.682326.57
90.50050.06850.0890.77020.2220.8470.01460.0205-0.00050.09420.0094-0.0446-0.024-0.0165-0.01490.04470.0115-0.01060.0630.01330.075210.911823.336826.5847
100.67780.37790.00621.53250.33190.6427-0.0139-0.0004-0.04020.08650.0373-0.0764-0.14150.04290.00080.17910.0287-0.02170.06660.0110.08536.039841.56340.3194
110.6214-0.12910.12170.5882-0.14870.4709-0.02290.0794-0.0822-0.0082-0.01070.03660.21230.04550.00820.15550.02430.01890.0934-0.01580.080622.4178-8.819627.3731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 167 )
3X-RAY DIFFRACTION3chain 'A' and (resid 168 through 300 )
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 431 )
5X-RAY DIFFRACTION5chain 'A' and (resid 432 through 464 )
6X-RAY DIFFRACTION6chain 'A' and (resid 465 through 520 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 166 )
8X-RAY DIFFRACTION8chain 'B' and (resid 167 through 300 )
9X-RAY DIFFRACTION9chain 'B' and (resid 301 through 396 )
10X-RAY DIFFRACTION10chain 'B' and (resid 397 through 464 )
11X-RAY DIFFRACTION11chain 'B' and (resid 465 through 519 )

+
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