[English] 日本語
Yorodumi
- PDB-7on9: Crystal structure of para-hydroxybenzoate-3-hydroxylase PraI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7on9
TitleCrystal structure of para-hydroxybenzoate-3-hydroxylase PraI
Components4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
KeywordsOXIDOREDUCTASE / P-HYDROXYBENZOATE HYDROXYLASE
Function / homology
Function and homology information


4-hydroxybenzoate 3-monooxygenase [NAD(P)H] / 4-hydroxybenzoate 3-monooxygenase [NAD(P)H] activity / 4-hydroxybenzoate 3-monooxygenase (NADH) activity / benzoate catabolic process / 4-hydroxybenzoate 3-monooxygenase (NADPH) activity / 4-hydroxybenzoate 3-monooxygenase activity / FAD binding / flavin adenine dinucleotide binding
Similarity search - Function
4-hydroxybenzoate 3-monooxygenase / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / P-HYDROXYBENZOIC ACID / 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
Similarity search - Component
Biological speciesPaenibacillus sp. JJ-1b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZahn, M. / McGeehan, J.E.
CitationJournal: Metab Eng / Year: 2022
Title: Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate.
Authors: Kuatsjah, E. / Johnson, C.W. / Salvachua, D. / Werner, A.Z. / Zahn, M. / Szostkiewicz, C.J. / Singer, C.A. / Dominick, G. / Okekeogbu, I. / Haugen, S.J. / Woodworth, S.P. / Ramirez, K.J. / ...Authors: Kuatsjah, E. / Johnson, C.W. / Salvachua, D. / Werner, A.Z. / Zahn, M. / Szostkiewicz, C.J. / Singer, C.A. / Dominick, G. / Okekeogbu, I. / Haugen, S.J. / Woodworth, S.P. / Ramirez, K.J. / Giannone, R.J. / Hettich, R.L. / McGeehan, J.E. / Beckham, G.T.
History
DepositionMay 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
B: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
C: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
D: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,27312
Polymers181,5794
Non-polymers3,6958
Water21,1501174
1
A: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
D: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6376
Polymers90,7892
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-29 kcal/mol
Surface area30990 Å2
MethodPISA
2
B: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
C: 4-hydroxybenzoate 3-monooxygenase (NAD(P)H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6376
Polymers90,7892
Non-polymers1,8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-27 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.11, 101.508, 106.849
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
4-hydroxybenzoate 3-monooxygenase (NAD(P)H) / 4-hydroxybenzoate 3-hydroxylase / 4HB 3-hydroxylase


Mass: 45394.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. JJ-1b (bacteria) / Gene: praI / Production host: Escherichia coli (E. coli)
References: UniProt: C4TP09, 4-hydroxybenzoate 3-monooxygenase [NAD(P)H]
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1174 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350 0.2 M ammonium citrate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.628→106.849 Å / Num. obs: 166829 / % possible obs: 95.2 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.039 / Net I/σ(I): 12.5
Reflection shellResolution: 1.628→1.731 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.853 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8343 / CC1/2: 0.49 / Rpim(I) all: 0.525 / % possible all: 62.4

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBE

1pbe


Resolution: 1.63→106.85 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.112
RfactorNum. reflection% reflectionSelection details
Rfree0.222 8351 -RANDOM
Rwork0.2035 ---
obs0.2044 166771 80.5 %-
Displacement parametersBiso mean: 26.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.1101 Å20 Å20 Å2
2--0.0589 Å20 Å2
3----0.169 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.63→106.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12370 0 252 1174 13796
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812962HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.917565HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4580SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2267HARMONIC5
X-RAY DIFFRACTIONt_it12962HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1618SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact12360SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion15.8
LS refinement shellResolution: 1.63→1.69 Å
RfactorNum. reflection% reflection
Rfree0.2493 157 -
Rwork0.2275 --
obs0.2286 3336 15.74 %
Refinement TLS params.

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)
10.6933-0.104-0.1060.2250.03990.6335-0.0113-0.0280.0504-0.0280.0090.02980.05040.02980.0023-0.0505-0.0118-0.0013-0.07990.0253-0.048-19.14529.2102-49.3093
20.5547-0.04740.22950.55750.04790.8438-0.01410.0093-0.00980.0093-0.0241-0.0626-0.0098-0.06260.0382-0.088-0.01520.0072-0.0737-0.0218-0.0452-55.369619.7079-46.285
30.6189-0.0878-0.21520.2737-0.01841.3785-0.04830.07050.08930.07050.0202-0.09770.0893-0.09770.0281-0.06660.01160.011-0.0709-0.0328-0.061-53.322232.2266-5.0052
41.03450.02970.17460.3191-0.02961.27480.00910.0623-0.07740.06230.0026-0.0639-0.0774-0.0639-0.0117-0.11230.0136-0.0076-0.03880.0566-0.1275-17.580121.3674-6.3004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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