[English] 日本語
Yorodumi
- PDB-1bkw: p-Hydroxybenzoate hydroxylase (phbh) mutant with cys116 replaced ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bkw
Titlep-Hydroxybenzoate hydroxylase (phbh) mutant with cys116 replaced by ser (c116s) and arg44 replaced by lys (r44k), in complex with fad and 4-hydroxybenzoic acid
ComponentsPROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
KeywordsOXIDOREDUCTASE / HYDROXYBENZOATE
Function / homology
Function and homology information


4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase [NADPH] activity / 4-hydroxybenzoate 3-monooxygenase activity / benzoate catabolic process via hydroxylation / FAD binding / flavin adenine dinucleotide binding
Similarity search - Function
4-hydroxybenzoate 3-monooxygenase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / P-HYDROXYBENZOIC ACID / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEppink, M.H. / Schreuder, H.A. / Van Berkel, W.J.
Citation
Journal: Eur.J.Biochem. / Year: 1995
Title: Structure and function of mutant Arg44Lys of 4-hydroxybenzoate hydroxylase implications for NADPH binding.
Authors: Eppink, M.H. / Schreuder, H.A. / Van Berkel, W.J.
#1: Journal: Protein Sci. / Year: 1994
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase Reconstituted with the Modified FAD Present in Alcohol Oxidase from Methyloprophic Yeasts: Evidence for an Arabinoflavin
Authors: Van Berkel, W.J. / Eppink, M.H. / Schreuder, H.A.
#2: Journal: Biochemistry / Year: 1994
Title: Crystal Structures of Wild-Type p-Hydroxybenzoate Hydroxylase Complexed with 4- Aminobenzoate, 2,4-Dihydroxybenzoate, and 2-Hydroxy-4-Aminobenzoate and the Tyr222Ala Mutant Complexed with 2- ...Title: Crystal Structures of Wild-Type p-Hydroxybenzoate Hydroxylase Complexed with 4- Aminobenzoate, 2,4-Dihydroxybenzoate, and 2-Hydroxy-4-Aminobenzoate and the Tyr222Ala Mutant Complexed with 2-Hydroxy-4-Aminobenzoate. Evidence for a Proton Channel and a New Binding Mode of the Flavin Ring
Authors: Schreuder, H.A. / Mattevi, A. / Obmolova, G. / Kalk, K.H. / Hol, W.G. / Van Der Bolt, F.J. / Van Berkel, W.J.
#3: Journal: Proteins / Year: 1992
Title: Crystal Structure of the Reduced Form of P-Hydroxybenzoate Hydroxylase Refined at 2.3 Angstroms Resolution
Authors: Schreuder, H.A. / Van Der Laan, J.M. / Swarte, M.B. / Kalk, K.H. / Hol, W.G. / Drenth, J.
#4: Journal: FEBS Lett. / Year: 1990
Title: Engineering of the Microheterogeneity-Resistant P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens
Authors: Eschrich, K. / Van Berkel, W.J. / Westphal, A.H. / De Kok, A. / Mattevi, A. / Obmolova, G. / Kalk, H. / Hol, W.G.
#5: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of the P-Hydroxybenzoate Hydroxylase-Substrate Complex Refined at 1.9 Angstroms Resolution. Analysis of the Enzyme-Substrate and Enzyme-Product Complexes
Authors: Schreuder, H.A. / Prick, P.A. / Wierenga, R.K. / Vriend, G. / Wilson, K.S. / Hol, W.G. / Drenth, J.
#6: Journal: Biochemistry / Year: 1989
Title: The Coenzyme Analogue Adenosine 5-Diphosphoribose Displaces FAD in the Active Site of P-Hydroxybenzoate Hydroxylase. An X-Ray Crystallographic Investigation
Authors: Van Der Laan, J.M. / Schreuder, H.A. / Swarte, M.B. / Wierenga, R.K. / Kalk, K.H. / Hol, W.G. / Drenth, J.
#7: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase Complexed with its Reaction Product 3,4-Dihydroxybenzoate
Authors: Schreuder, H.A. / Van Der Laan, J.M. / Hol, W.G. / Drenth, J.
#8: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase
Authors: Wierenga, R.K. / De Jong, R.J. / Kalk, K.H. / Hol, W.G. / Drenth, J.
#9: Journal: J.Biol.Chem. / Year: 1975
Title: Crystallization and Preliminary X-Ray Investigation of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens
Authors: Drenth, J. / Hol, W.G.J. / Wierenga, R.K.
History
DepositionJul 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 22, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 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 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2603
Polymers44,3361
Non-polymers9242
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
hetero molecules

A: PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5206
Polymers88,6732
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6300 Å2
ΔGint-32 kcal/mol
Surface area30470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.700, 146.400, 88.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein PROTEIN (P-HYDROXYBENZOATE HYDROXYLASE)


Mass: 44336.492 Da / Num. of mol.: 1 / Mutation: R44K, C116S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Plasmid: PUC9 / Gene (production host): POBA / Production host: Escherichia coli (E. coli) / Strain (production host): TG2
References: UniProt: P00438, 4-hydroxybenzoate 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID / 4-Hydroxybenzoic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7
Details: 39% AMMONIUMSULFATE, 100 MM SODIUM PHOSPHATE, 0.04 MM FAD, 0.15 MM EDTA, 60 MM SODIUM SULFITE, 1 MM P-HYDROXYBENZOATE, pH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMpotassium phosphate1droppH7.0
339 %satammonium sulfate1reservoir
40.14 mMFAD1reservoir
50.15 mMEDTA1reservoir
61 mM4-hydroxybenzoate1reservoir
760 mMsodium sulfite1reservoir
8100 mMpotassium phosphate1reservoirpH7.0

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 15, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→8 Å / Num. obs: 23336 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.068 / Net I/σ(I): 12
Reflection
*PLUS
Num. measured all: 92992 / Rmerge(I) obs: 0.068

-
Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLORmodel building
X-PLOR3.8refinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBE

1pbe


Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rwork0.182 --
obs0.182 23336 96.6 %
Displacement parametersBiso mean: 28.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 63 243 3402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2FAD.PARFAD.TOP
X-RAY DIFFRACTION3WAT.PARPHB.TOP
X-RAY DIFFRACTION4WAT.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

+
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