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- PDB-7w6v: Crystal structure of a dicobalt-substituted small laccase at 2.47... -

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Basic information

Entry
Database: PDB / ID: 7w6v
TitleCrystal structure of a dicobalt-substituted small laccase at 2.47 angstrom
ComponentsPutative copper oxidase
KeywordsOXIDOREDUCTASE / cobalt-binding / metalloenzyme
Function / homology
Function and homology information


oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsYang, X. / Wu, F. / Wu, W. / Chen, X. / Fan, S. / Yu, P. / Mao, L.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFE0200800, 2018YFA0703501, 2016YFA0200104 China
National Natural Science Foundation of China (NSFC)21790390, 21790391, 22134002, 21874139, 21927804, 22104140 China
Chinese Academy of Sciences China
CitationJournal: Sci Adv / Year: 2022
Title: A versatile artificial metalloenzyme scaffold enabling direct bioelectrocatalysis in solution.
Authors: Yang, X. / Wu, W. / Chen, X. / Wu, F. / Fan, S. / Yu, P. / Mao, L.
History
DepositionDec 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7263
Polymers30,6081
Non-polymers1182
Water1,54986
1
A: Putative copper oxidase
hetero molecules

A: Putative copper oxidase
hetero molecules

A: Putative copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1789
Polymers91,8253
Non-polymers3546
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11710 Å2
ΔGint-130 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.030, 178.030, 178.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Putative copper oxidase


Mass: 30608.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO6712 / Plasmid: pET20b / Production host: Escherichia coli #1/H766 (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9XAL8
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 7.68 Å3/Da / Density % sol: 83.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2% v/v PEG 400, 2.0 M ammonium sulfate, 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jan 13, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 35302 / % possible obs: 100 % / Redundancy: 73.5 % / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.202 / Χ2: 0.78 / Net I/σ(I): 3.4 / Num. measured all: 2595911
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.47-2.5154.53.49217120.7080.4743.5240.432
2.51-2.56613.25717170.770.4183.2840.419
2.56-2.6165.63.05917410.810.3783.0830.421
2.61-2.6667.32.58517420.8780.3162.6050.437
2.66-2.7268.32.01717030.8980.2452.0320.499
2.72-2.7876.51.80217390.9450.2061.8130.476
2.78-2.8579.81.50117310.9630.1681.5110.495
2.85-2.93801.0517470.9780.1181.0570.455
2.93-3.0179.40.81217380.9860.0910.8180.461
3.01-3.1178.30.64717440.9910.0730.6510.476
3.11-3.2276.50.47717390.9950.0550.480.513
3.22-3.3571.70.35217500.9960.0420.3540.565
3.35-3.579.50.2617590.9980.0290.2620.672
3.5-3.6980.50.20517590.9980.0230.2070.739
3.69-3.9279.30.16217720.9990.0180.1630.863
3.92-4.2276.60.12117790.9990.0140.1211.026
4.22-4.6574.40.09717870.9990.0110.0981.275
4.65-5.3279.50.08518130.9990.010.0861.231
5.32-6.771.90.078184110.0090.0781.189
6.7-5069.70.06519890.9990.0080.0652.571

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CG8

3cg8


Resolution: 2.47→49.43 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.456 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 1733 4.9 %RANDOM
Rwork0.1863 ---
obs0.1869 33489 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 179.76 Å2 / Biso mean: 58.494 Å2 / Biso min: 35.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.47→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 2 86 2241
Biso mean--85.37 55.91 -
Num. residues----280
LS refinement shellResolution: 2.47→2.531 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.34 110 -
Rwork0.35 2431 -
obs--100 %

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