[English] 日本語
Yorodumi
- PDB-2phh: THE COENZYME ANALOGUE ADENOSINE 5-DIPHOSPHORIBOSE DISPLACES FAD I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2phh
TitleTHE COENZYME ANALOGUE ADENOSINE 5-DIPHOSPHORIBOSE DISPLACES FAD IN THE ACTIVE SITE OF P-HYDROXYBENZOATE HYDROXYLASE. AN X-RAY CRYSTALLOGRAPHIC INVESTIGATION
ComponentsP-HYDROXYBENZOATE HYDROXYLASE
KeywordsOXIDOREDUCTASE
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
ADENOSINE-5-DIPHOSPHORIBOSE / P-HYDROXYBENZOIC ACID / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsVan Derlaan, J.M. / Drenth, J. / Hol, W.G.J.
Citation
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.
#1: Journal: Eur.J.Biochem. / Year: 1989
Title: The Influence of Purification and Protein Heterogeneity on the Crystallization of P-Hydroxybenzoate Hydroxylase
Authors: Van Derlaan, J.M. / Swarte, M.B.A. / Groendijk, H. / Hol, W.G.J. / Drenth, J.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of the P-Hydroxylase-Substrate Complex Refined at 1.9 Angstroms Resolution
Authors: Schreuder, H.A. / Prick, P.A.J. / Wierenga, R.K. / Vriend, G. / Wilson, K.S. / Hol, W.G.J. / Drenth, J.
#3: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylas Complexed with its Reaction Product 3,4-Dihydroxybenzoate
Authors: Schreuder, H.A. / Van Derlaan, J.M. / Hol, W.G.J. / Drenth, J.
#4: Journal: Eur.J.Biochem. / Year: 1983
Title: P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. 1. Completion of the Elucidation of the Primary Structure
Authors: Hofsteenge, J. / Weijer, W.J. / Jekel, P.A. / Beintema, J.J.
#5: Journal: Eur.J.Biochem. / Year: 1983
Title: P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. 2. Fitting of the Amino-Acid Sequence to the Tertiary Structure
Authors: Weijer, W.J. / Hofsteenge, J. / Beintema, J.J. / Wierenga, R.K. / Drenth, J.
#6: Journal: J.Mol.Biol. / Year: 1983
Title: Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase
Authors: Wierenga, R.K. / Drenth, J. / Schulz, G.E.
#7: Journal: Eur.J.Biochem. / Year: 1980
Title: Primary and Tertiary Structure Studies of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. Isolation and Alignment of the Cnbr Peptides. Interactions of the Protein with Flavin Adenine Dinucleotide
Authors: Hofsteenge, J. / Vereijken, J.M. / Weijer, W.J. / Beintema, J.J. / Wierenga, R.K. / Drenth, J.
#8: Journal: Eur.J.Biochem. / Year: 1980
Title: The Amino-Acid Sequence of the Three Smallest Cnbr Peptides from P-Hydroxybenzoate Hydroxylase from Pseudomonas Florescens
Authors: Vereijken, J.M. / Hofsteenge, J. / Bak, H.J. / Beintema, J.J.
#9: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase
Authors: Wierenga, R.K. / Dejong, R.J. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
#10: Journal: J.Biol.Chem. / Year: 1975
Title: Crystallization and Preliminary X-Ray Investigation of P-Hydrobenzoate Hydroxylase from Pseudomonas Fluorescens
Authors: Drenth, J. / Hol, W.G.J. / Wierenga, R.K.
History
DepositionJun 19, 1989Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0783
Polymers44,3811
Non-polymers6972
Water1,02757
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1566
Polymers88,7612
Non-polymers1,3954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5470 Å2
ΔGint-33 kcal/mol
Surface area31210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.700, 146.400, 89.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUE 275 IS A CIS-PROLINE.

-
Components

#1: Protein P-HYDROXYBENZOATE HYDROXYLASE


Mass: 44380.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria)
References: UniProt: P00438, 4-hydroxybenzoate 3-monooxygenase
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#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.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.2 mg/mlenzyme 11
2100 mMpotasssium phosphate11
31 mMenzyme complex(pOHB)11
40.02 mMFAD11
50.15 mMEDTA11
60.10 mMGSH11
760 mMadenosine 5-diphosphoribose11
870 %satammonium sulfate12
9100 mMpotassium phisphate12
101 mMpOHB12
110.02 mMFAD12
120.15 mMEDTA12
130.10 mMGSH12
141.0 M12Na2S2O4

-
Data collection

Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 9857 / % possible obs: 70 % / Num. measured all: 19604 / Rmerge(I) obs: 0.066

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.168 / Highest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 46 57 3201
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8674
X-RAY DIFFRACTIONp_mcangle_it3.9574
X-RAY DIFFRACTIONp_scbond_it6.7496
X-RAY DIFFRACTIONp_scangle_it8.7739
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1750.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.2
X-RAY DIFFRACTIONp_multtor_nbd0.1940.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1860.2
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
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 6 Å / Rfactor obs: 0.168 / Num. reflection obs: 8836
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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