[English] 日本語
Yorodumi
- PDB-5v2d: Crystal structure of Pseudomonas brassicacearum lignostilbene dio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v2d
TitleCrystal structure of Pseudomonas brassicacearum lignostilbene dioxygenase
ComponentsDioxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / ligonostilbene / carotenoids
Function / homologyCarotenoid oxygenase / Retinal pigment epithelial membrane protein / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / Quinoprotein alcohol dehydrogenase-like superfamily / metal ion binding / : / Dioxygenase
Function and homology information
Biological speciesPseudomonas brassicacearum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLoewen, P.C. / Loewen, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)D9600 Canada
CitationJournal: BMC Biochem. / Year: 2018
Title: Structure and function of a lignostilbene-alpha , beta-dioxygenase orthologue from Pseudomonas brassicacearum.
Authors: Loewen, P.C. / Switala, J. / Wells, J.P. / Huang, F. / Zara, A.T. / Allingham, J.S. / Loewen, M.C.
History
DepositionMar 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dioxygenase
B: Dioxygenase
C: Dioxygenase
D: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,5118
Polymers224,2884
Non-polymers2234
Water19,3841076
1
A: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1282
Polymers56,0721
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1282
Polymers56,0721
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1282
Polymers56,0721
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1282
Polymers56,0721
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.397, 104.673, 104.709
Angle α, β, γ (deg.)90.000, 94.790, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA-1 - 48019 - 500
21PROPROBB-1 - 48019 - 500
12PROPROAA2 - 48022 - 500
22PROPROCC2 - 48022 - 500
13PROPROAA2 - 48022 - 500
23PROPRODD2 - 48022 - 500
14PROPROBB2 - 48022 - 500
24PROPROCC2 - 48022 - 500
15PROPROBB2 - 48022 - 500
25PROPRODD2 - 48022 - 500
16GLYGLYCC2 - 48122 - 501
26GLYGLYDD2 - 48122 - 501

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Dioxygenase


Mass: 56071.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas brassicacearum (bacteria) / Gene: CD58_10895 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: W8QAY8
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1076 / 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: 2.41 Å3/Da / Density % sol: 48.94 % / Mosaicity: 0.24 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 24% PEG 3350, Bis-Tris 100 mM

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2016 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→104.343 Å / Num. all: 161021 / Num. obs: 161021 / % possible obs: 99 % / Redundancy: 3.1 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.056 / Rsym value: 0.046 / Net I/av σ(I): 14.1 / Net I/σ(I): 16.1 / Num. measured all: 495497
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-230.4951.571989236800.3410.6030.4952.599.8
2-2.1230.3072.568095223540.2110.3740.307499.7
2.12-2.273.10.2033.764130209840.1380.2460.203699.5
2.27-2.453.10.1365.559805194990.0930.1650.1368.699.4
2.45-2.693.10.0918.255273180000.0620.1110.09112.399.3
2.69-33.10.05513.549879161680.0370.0670.05519.199
3-3.473.10.0322244111141770.0210.0380.0323098.3
3.47-4.253.10.02229.937252118850.0150.0270.02241.597.4
4.25-6.013.20.01835.22906791950.0120.0220.01847.997
6.01-48.033.10.01827.91589650790.0120.0220.01850.396.4

-
Processing

Software
NameVersionClassification
REFMACrefinement
SCALA3.3.22data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 2BIW

2biw


Resolution: 1.9→48.03 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1781 / WRfactor Rwork: 0.1487 / FOM work R set: 0.8522 / SU B: 6.793 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1359 / SU Rfree: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 8106 5 %RANDOM
Rwork0.1613 ---
obs0.1629 152884 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.21 Å2 / Biso mean: 34.147 Å2 / Biso min: 17.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20.64 Å2
2--1.06 Å20 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.9→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15281 0 4 1076 16361
Biso mean--22.14 36.57 -
Num. residues----1931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01915866
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214124
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.95521623
X-RAY DIFFRACTIONr_angle_other_deg1.119332775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06751945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11123.543796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.527152343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.04415113
X-RAY DIFFRACTIONr_chiral_restr0.1580.22245
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02118002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023487
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A319780.06
12B319780.06
21A317400.06
22C317400.06
31A318700.05
32D318700.05
41B318480.06
42C318480.06
51B318520.05
52D318520.05
61C316780.05
62D316780.05
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 622 -
Rwork0.264 11383 -
all-12005 -
obs--99.82 %
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)
10.5165-0.3925-0.02530.35750.15040.3818-0.08060.04080.05550.0968-0.0297-0.01510.0585-0.05420.11030.0380.0042-0.00650.038-0.0170.0577-0.3343-0.992551.0106
20.2077-0.1919-0.13470.21790.18990.49750.05410.02310.0317-0.024-0.0177-0.04750.0233-0.1154-0.03650.03230.00790.00290.06590.02290.03817.3476-19.07989.8774
30.2419-0.12670.3070.1469-0.1131.33930.01620.031-0.15210.01330.09780.0931-0.33860.272-0.11410.1362-0.0473-0.02110.16170.00810.1015-49.386815.551443.8589
40.1459-0.14170.10120.4347-0.16410.3453-0.01880.0618-0.00210.03940.00710.02230.0372-0.02110.01170.0369-0.02330.00580.05480.00040.027731.7732-67.5062.6679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 500
2X-RAY DIFFRACTION2B-1 - 500
3X-RAY DIFFRACTION3C2 - 500
4X-RAY DIFFRACTION4D2 - 500

+
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