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- PDB-5v2d: Crystal structure of Pseudomonas brassicacearum lignostilbene dio... -

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Basic information

Entry
Database: PDB / ID: 5v2d
TitleCrystal structure of Pseudomonas brassicacearum lignostilbene dioxygenase
ComponentsDioxygenase
KeywordsOXIDOREDUCTASE / dioxygenase / ligonostilbene / carotenoids
Function / homologyOxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

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

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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 / Iron


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


Mass: 18.015 Da / Num. of mol.: 1076 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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

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