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- PDB-8aip: Crystal Structure of Two-domain bacterial laccase from the actino... -

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Basic information

Entry
Database: PDB / ID: 8aip
TitleCrystal Structure of Two-domain bacterial laccase from the actinobacterium Streptomyces carpinensis VKM Ac-1300
ComponentsTwo-Domain Laccase
KeywordsOXIDOREDUCTASE / Two-Domain Laccase / laccase / Streptomyces carpinensis
Function / homologyCOPPER (II) ION / OXYGEN MOLECULE
Function and homology information
Biological speciesStreptomyces carpinensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V. / Trubitsina, L. / Trubitsin, I. / Leontievsky, A. / Lisov, A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Federation President Grant Russian Federation
CitationJournal: Biochemistry Mosc. / Year: 2023
Title: A Novel Two-Domain Laccase with Middle Redox Potential: Physicochemical and Structural Properties.
Authors: Trubitsina, L.I. / Trubitsin, I.V. / Lisov, A.V. / Gabdulkhakov, A.G. / Zavarzina, A.G. / Belova, O.V. / Larionova, A.P. / Tishchenko, S.V. / Leontievsky, A.A.
History
DepositionJul 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Two-Domain Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4495
Polymers32,2261
Non-polymers2234
Water1,49583
1
A: Two-Domain Laccase
hetero molecules

A: Two-Domain Laccase
hetero molecules

A: Two-Domain Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,34615
Polymers96,6783
Non-polymers66812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area12060 Å2
ΔGint-122 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.962, 97.962, 97.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

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Components

#1: Protein Two-Domain Laccase


Mass: 32226.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VKM Ac-1300 / Source: (gene. exp.) Streptomyces carpinensis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 20%v/v PEG Smear Broad, 0.1 M Sodium citratate, pH 5.6, 0.15 M Mg acetate (condition #33 of BCS-1 from Molecular Dimensions, UK)

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→33 Å / Num. obs: 13826 / % possible obs: 97 % / Redundancy: 4.29 % / Biso Wilson estimate: 30.39 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.075 / Net I/σ(I): 6.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1147 / CC1/2: 0.8 / % possible all: 82.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.20.1_4487refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GYB

4gyb


Resolution: 2.35→32.65 Å / SU ML: 0.3312 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.6689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2814 642 4.91 %
Rwork0.2312 12423 -
obs0.2337 13065 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.3 Å2
Refinement stepCycle: LAST / Resolution: 2.35→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 5 83 2210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872181
X-RAY DIFFRACTIONf_angle_d0.95742960
X-RAY DIFFRACTIONf_chiral_restr0.0616311
X-RAY DIFFRACTIONf_plane_restr0.0089393
X-RAY DIFFRACTIONf_dihedral_angle_d12.3493297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.530.36481220.27552341X-RAY DIFFRACTION94.15
2.53-2.790.37861240.27582498X-RAY DIFFRACTION99.47
2.79-3.190.34721210.29132484X-RAY DIFFRACTION98.64
3.19-4.020.30781400.25742475X-RAY DIFFRACTION98.35
4.02-32.650.18861350.16332625X-RAY DIFFRACTION99.24
Refinement TLS params.Method: refined / Origin x: 38.8202093805 Å / Origin y: -15.2701824309 Å / Origin z: 20.310484471 Å
111213212223313233
T0.13453948993 Å2-0.0102043533202 Å20.0232484340473 Å2-0.144450890116 Å2-0.029398664992 Å2--0.142040969382 Å2
L0.199702573787 °20.0705176685383 °2-0.152040877917 °2-0.172779671092 °2-0.0866910285589 °2--0.319951929308 °2
S0.000973593263586 Å °-0.00335512888963 Å °0.0230746161887 Å °-0.00352928838348 Å °-0.00823715003303 Å °-0.0592230751704 Å °-0.0383885551218 Å °-3.59448276144E-5 Å °6.95142947502E-11 Å °
Refinement TLS groupSelection details: all

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