[English] 日本語
Yorodumi
- PDB-4zxa: Crystal Structure of hydroquinone 1,2-dioxygenase PnpCD in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zxa
TitleCrystal Structure of hydroquinone 1,2-dioxygenase PnpCD in complex with Cd2+ and 4-hydroxybenzonitrile
Components
  • Hydroquinone dioxygenase large subunit
  • Hydroquinone dioxygenase small subunit
KeywordsOXIDOREDUCTASE / dioxygenase / hydroquinone pathway / cupin
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
Hydroquinone 1,2-dioxygenase large subunit, N-terminal / Hydroquinone 1,2-dioxygenase large subunit N-terminal / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / 4-hydroxybenzonitrile / Hydroquinone dioxygenase large subunit / Hydroquinone dioxygenase small subunit
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.488 Å
AuthorsLiu, S. / Su, T. / Zhang, C. / Gu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31070655 China
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of PnpCD, a Two-subunit Hydroquinone 1,2-Dioxygenase, Reveals a Novel Structural Class of Fe2+-dependent Dioxygenases.
Authors: Liu, S. / Su, T. / Zhang, C. / Zhang, W.M. / Zhu, D. / Su, J. / Wei, T. / Wang, K. / Huang, Y. / Guo, L. / Xu, S. / Zhou, N.Y. / Gu, L.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydroquinone dioxygenase small subunit
B: Hydroquinone dioxygenase small subunit
C: Hydroquinone dioxygenase small subunit
D: Hydroquinone dioxygenase small subunit
W: Hydroquinone dioxygenase large subunit
X: Hydroquinone dioxygenase large subunit
Y: Hydroquinone dioxygenase large subunit
Z: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,67416
Polymers226,7488
Non-polymers9268
Water12,953719
1
A: Hydroquinone dioxygenase small subunit
B: Hydroquinone dioxygenase small subunit
W: Hydroquinone dioxygenase large subunit
X: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8378
Polymers113,3744
Non-polymers4634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15020 Å2
ΔGint-94 kcal/mol
Surface area36600 Å2
MethodPISA
2
C: Hydroquinone dioxygenase small subunit
D: Hydroquinone dioxygenase small subunit
Y: Hydroquinone dioxygenase large subunit
Z: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8378
Polymers113,3744
Non-polymers4634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-95 kcal/mol
Surface area36700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.023, 181.048, 186.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Hydroquinone dioxygenase small subunit


Mass: 18308.932 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (strain WBC-3) (bacteria)
Strain: WBC-3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1I210
#2: Protein
Hydroquinone dioxygenase large subunit


Mass: 38377.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (strain WBC-3) (bacteria)
Strain: WBC-3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1I209
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-H8N / 4-hydroxybenzonitrile


Mass: 119.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H5NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium thiocyanate, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.488→50 Å / Num. obs: 92003 / % possible obs: 100 % / Redundancy: 7.2 % / Rsym value: 0.102 / Net I/σ(I): 29.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 5.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.488→40.732 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 4435 5.01 %Random
Rwork0.1865 ---
obs0.189 88538 95.83 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.296 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.6618 Å20 Å2-0 Å2
2--9.2656 Å20 Å2
3----3.6038 Å2
Refinement stepCycle: LAST / Resolution: 2.488→40.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15448 0 40 719 16207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815997
X-RAY DIFFRACTIONf_angle_d1.06721734
X-RAY DIFFRACTIONf_dihedral_angle_d16.1525781
X-RAY DIFFRACTIONf_chiral_restr0.0722284
X-RAY DIFFRACTIONf_plane_restr0.0052869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4883-2.51650.3271200.23942194X-RAY DIFFRACTION76
2.5165-2.54610.2961410.23082583X-RAY DIFFRACTION91
2.5461-2.57720.28871210.22572656X-RAY DIFFRACTION90
2.5772-2.60980.28041450.2372598X-RAY DIFFRACTION91
2.6098-2.64410.3011360.23172667X-RAY DIFFRACTION92
2.6441-2.68040.27961490.23112657X-RAY DIFFRACTION93
2.6804-2.71860.34481260.22842704X-RAY DIFFRACTION93
2.7186-2.75920.31891530.21872716X-RAY DIFFRACTION93
2.7592-2.80230.24891370.20582751X-RAY DIFFRACTION95
2.8023-2.84820.27911420.22172742X-RAY DIFFRACTION94
2.8482-2.89730.28041660.22262674X-RAY DIFFRACTION94
2.8973-2.950.28391600.21832771X-RAY DIFFRACTION95
2.95-3.00670.27231410.21462782X-RAY DIFFRACTION96
3.0067-3.06810.30251530.21432786X-RAY DIFFRACTION96
3.0681-3.13480.28731640.20342792X-RAY DIFFRACTION97
3.1348-3.20770.25741450.20982861X-RAY DIFFRACTION97
3.2077-3.28790.26631410.20122840X-RAY DIFFRACTION99
3.2879-3.37670.24711480.20542906X-RAY DIFFRACTION99
3.3767-3.4760.26491620.19662865X-RAY DIFFRACTION99
3.476-3.58820.26711320.19582892X-RAY DIFFRACTION99
3.5882-3.71630.24031390.18352956X-RAY DIFFRACTION99
3.7163-3.8650.22621680.18642895X-RAY DIFFRACTION99
3.865-4.04080.22641280.16892919X-RAY DIFFRACTION99
4.0408-4.25360.18971690.14942907X-RAY DIFFRACTION99
4.2536-4.51980.15491360.13262950X-RAY DIFFRACTION100
4.5198-4.86820.1851730.13422927X-RAY DIFFRACTION100
4.8682-5.35720.20131760.1512933X-RAY DIFFRACTION100
5.3572-6.13010.20071430.1743000X-RAY DIFFRACTION100
6.1301-7.71470.21471470.18223048X-RAY DIFFRACTION100
7.7147-40.73730.19191740.17813131X-RAY DIFFRACTION99

+
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