[English] 日本語
Yorodumi
- PDB-5zyr: Crystal structure of the reductase (C1) component of p-hydroxyphe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zyr
TitleCrystal structure of the reductase (C1) component of p-hydroxyphenylacetate 3-hydroxylase (HPAH) from Acinetobacter baumannii
Componentsp-hydroxyphenylacetate 3-hydroxylase, reductase component
KeywordsFLAVOPROTEIN / Reductase / Monooxygenase / Acinetobacter baumannii
Function / homology
Function and homology information


flavin reductase (NADH) / flavin reductase (NADH) activity / riboflavin reductase (NADPH) activity / : / FMN binding
Similarity search - Function
Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / FMN-binding split barrel / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / p-hydroxyphenylacetate 3-hydroxylase, reductase component
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.20001320062 Å
AuthorsOonanant, W. / Phongsak, T. / Sucharitakul, J. / Chaiyen, P. / Yuvaniyama, J.
Funding support Thailand, 2items
OrganizationGrant numberCountry
Synchrotron Light Research Institute2-2549/LS02 Thailand
Thailand
Citation
Journal: To Be Published
Title: Crystal structure of the reductase (C1) component of p-hydroxyphenylacetate 3-hydroxylase (HPAH) from Acinetobacter baumannii
Authors: Oonanant, W. / Phongsak, T. / Sucharitakul, J. / Chaiyen, P. / Yuvaniyama, J.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2012
Title: Crystallization and preliminary X-ray analysis of the reductase component of p-hydroxyphenylacetate 3-hydroxylase from Acinetobacter baumannii
Authors: Oonanant, W. / Sucharitakul, J. / Chaiyen, P. / Yuvaniyama, J.
#2: Journal: J. Biol. Chem. / Year: 2012
Title: The C-terminal domain of 4-hydroxyphenylacetate 3-hydroxylase from Acinetobacter baumannii is an autoinhibitory domain
Authors: Phongsak, T. / Sucharitakul, J. / Thotsaporn, K. / Oonanant, W. / Yuvaniyama, J. / Svasti, J. / Ballou, D.P. / Chaiyen, P.
#3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionMay 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: p-hydroxyphenylacetate 3-hydroxylase, reductase component
B: p-hydroxyphenylacetate 3-hydroxylase, reductase component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9416
Polymers70,9102
Non-polymers1,0314
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14010 Å2
ΔGint-104 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.992, 59.900, 212.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein p-hydroxyphenylacetate 3-hydroxylase, reductase component / 4-HPA 3-monooxygenase small component / Flavin:NAD(+) oxidoreductase / p-hydroxyphenylacetate 3- ...4-HPA 3-monooxygenase small component / Flavin:NAD(+) oxidoreductase / p-hydroxyphenylacetate 3-hydroxylase C1 component


Mass: 35455.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: C1-hpah / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q271, flavin reductase (NADH)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.21 Å3/Da / Density % sol: 44.42 % / Description: Yellow rod shape with a tapered end
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6 / Details: PEG 400, sodium acetate, glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 31616 / % possible obs: 97.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 42.81 Å2 / Rmerge(I) obs: 0.119 / Χ2: 0.981 / Net I/σ(I): 9.45
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 2591 / Χ2: 0.768 / % possible all: 81.2

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
CNSv1.2phasing
Coot0.8.8model building
PHENIX1.11.1_2575refinement
RefinementMethod to determine structure: MAD / Resolution: 2.20001320062→29.9528 Å / SU ML: 0.273500794138 / Cross valid method: FREE R-VALUE / σ(F): 1.33649246174 / Phase error: 23.0556794462
Details: Atoms with zero occupancy have unobserved density and are modeled with the most probable rotamer that does not clash with other surrounding atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.218998393315 1648 5.2643347708 %Random selection
Rwork0.169797216896 ---
obs0.172348253032 31305 97.6998938893 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.3670044805 Å2
Refinement stepCycle: LAST / Resolution: 2.20001320062→29.9528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4846 0 70 127 5043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008701482553525033
X-RAY DIFFRACTIONf_angle_d0.9377442499966805
X-RAY DIFFRACTIONf_chiral_restr0.0544765395634740
X-RAY DIFFRACTIONf_plane_restr0.0062060904545876
X-RAY DIFFRACTIONf_dihedral_angle_d20.83232189513008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.20001320062-2.26470.2768115814051180.2335803792562090X-RAY DIFFRACTION84.0182648402
2.2647-2.33780.2798205341491560.2197432624112317X-RAY DIFFRACTION95.4457738325
2.3378-2.42130.3078711059861330.2186893656022458X-RAY DIFFRACTION98.330170778
2.4213-2.51820.2695465009891440.2015377422352488X-RAY DIFFRACTION99.696969697
2.5182-2.63280.2572890126851470.1865879151012473X-RAY DIFFRACTION100
2.6328-2.77150.2671641236041410.187214549612487X-RAY DIFFRACTION100
2.7715-2.9450.2496445054281320.1948805416582539X-RAY DIFFRACTION99.925177703
2.945-3.17210.2201883693841390.1931485136542516X-RAY DIFFRACTION99.9247271359
3.1721-3.49090.2733399453971200.1781076698842556X-RAY DIFFRACTION99.6648044693
3.4909-3.99510.192715982381510.1571714572632535X-RAY DIFFRACTION99.518340126
3.9951-5.02950.1832358137961400.1341317336732531X-RAY DIFFRACTION98.6701145179
5.0295-29.95280.1764599768421270.1584063253222667X-RAY DIFFRACTION97.0813064628
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)
12.29617387267-0.631975720477-0.3177831320162.444812784-0.1073039205513.61807047574-0.0814482480612-0.4809950293470.3158533516530.315224576896-0.02901864049560.208715910534-0.148614370913-0.299691002780.1003833756790.286691460845-0.03847519266260.01459825459890.40961421985-0.1029664772820.36911588482813.92221926925.4651738422940.2655195443
22.07617255723-5.29942862204-3.515188935377.778819694075.724543461532.058501884210.4369391472011.21316526313-0.264159639852-0.188836916959-0.0190349896359-0.2157874356340.3284913596420.513895407958-0.239299492030.4692550024990.02950137288230.01235198066160.540230464621-0.06328481334880.46129690991313.8043951032-13.00220446745.9216172557
34.608328203551.095075238623.461830765061.624959925682.035351046136.55899943193-0.1463271168970.1844245191490.411566929737-0.305205333045-0.0318336145769-0.216355850695-0.4332079637120.4990443979030.1715963562840.363182931819.56984777837E-50.06681289800620.2812325018070.09407539153060.43285495890430.57655178958.5624399437115.6907952396
43.01018990256-0.106824077990.3921527390712.283770952070.1349359806223.246979971040.0112742280279-0.343926452907-0.4649311334910.193065416183-0.036394031540.1127283945260.553939502866-0.1223511602120.02479230812510.35560347299-0.0518217222410.02539197014690.2990045704930.04092672091240.35275331261520.7407588985-14.595407618435.6953322206
52.04740615663-5.21522468642-0.3986508059415.419394273971.483122957983.906055072330.2204049702341.053118101531.37488749212-0.311953542997-0.2146518357030.201601678261-0.554553403654-0.3569202361630.08747849590480.4481101259940.0168632122739-0.008889264906470.3744887717160.132626623640.64725601499224.241107674416.657480695913.4270792238
64.389309002741.6534748904-1.55741766082.93182299596-1.68709008024.36257731627-0.114882019270.109370753605-0.176582242347-0.399035835565-0.02406304243130.2631076185190.266884805278-0.5915182934210.1356543056730.3295418374530.0322958434352-0.07007345956680.352476273173-0.1301356205960.3237356417716.77384865506-6.4344436589110.7693445054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:168)
2X-RAY DIFFRACTION2(chain A and resid 169:190)
3X-RAY DIFFRACTION3(chain A and resid 191:315)
4X-RAY DIFFRACTION4(chain B and resid 10:168)
5X-RAY DIFFRACTION5(chain B and resid 169:190)
6X-RAY DIFFRACTION6(chain B and resid 191:315)

+
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://pdbjlvh1.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