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- PDB-6l3w: Crystal structure of BphC, a halotolerant catechol dioxygenase -

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Basic information

Entry
Database: PDB / ID: 6l3w
TitleCrystal structure of BphC, a halotolerant catechol dioxygenase
ComponentsExtra-diol dioxygenase BphC
KeywordsOXIDOREDUCTASE / Dioxygenase / catechol / metalloproteins / halotolerant
Function / homology2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta / :
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsThakur, K.G. / Solanki, V.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research India
CitationJournal: mSystems / Year: 2019
Title: Structure Elucidation and Biochemical Characterization of Environmentally Relevant Novel Extradiol Dioxygenases Discovered by a Functional Metagenomics Approach.
Authors: Sidhu, C. / Solanki, V. / Pinnaka, A.K. / Thakur, K.G.
History
DepositionOct 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Extra-diol dioxygenase BphC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3102
Polymers35,2541
Non-polymers561
Water2,720151
1
A: Extra-diol dioxygenase BphC
hetero molecules

A: Extra-diol dioxygenase BphC
hetero molecules

A: Extra-diol dioxygenase BphC
hetero molecules

A: Extra-diol dioxygenase BphC
hetero molecules

A: Extra-diol dioxygenase BphC
hetero molecules

A: Extra-diol dioxygenase BphC
hetero molecules

A: Extra-diol dioxygenase BphC
hetero molecules

A: Extra-diol dioxygenase BphC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,47816
Polymers282,0318
Non-polymers4478
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Unit cell
Length a, b, c (Å)98.640, 98.640, 158.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

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Components

#1: Protein Extra-diol dioxygenase BphC


Mass: 35253.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Gene: 2,3-dihydroxybiphenyl 1,2-dioxygenase / Plasmid: pET28a / Cell (production host): BL21-DE3 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsAUTHORS STATE THAT THE NCBI ACCESSION NUMBER IS KX965751 FOR THIS SEQUENCE.

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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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M sodium citrate pH 6.0, 2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→31.19 Å / Num. obs: 12365 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.068 / Rrim(I) all: 0.157 / Rsym value: 0.141 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.6-2.745.30.50917720.8310.020.0440.03999.7
8.22-31.194.80.0394250.9980.0310.0730.06695.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
iMOSFLM3.3.22data reduction
SCALA3.3.22data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HAN

1han


Resolution: 2.6→31.19 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.884 / SU B: 10.355 / SU ML: 0.214 / SU R Cruickshank DPI: 0.6048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.605 / ESU R Free: 0.302
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 581 4.7 %RANDOM
Rwork0.194 ---
obs0.1965 11784 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.22 Å2 / Biso mean: 23.993 Å2 / Biso min: 1.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.6→31.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 1 151 2496
Biso mean--56.74 18.88 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0142412
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172102
X-RAY DIFFRACTIONr_angle_refined_deg0.881.6443277
X-RAY DIFFRACTIONr_angle_other_deg0.7291.6294926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.12621.053133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2911519
X-RAY DIFFRACTIONr_chiral_restr0.0430.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 44 -
Rwork0.254 860 -
all-904 -
obs--99.45 %

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