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- PDB-9bd5: Laccase from Bacillus licheniformis -

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Basic information

Entry
Database: PDB / ID: 9bd5
TitleLaccase from Bacillus licheniformis
ComponentsSpore coat protein A
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Spore coat protein A
Similarity search - Component
Biological speciesBacillus paralicheniformis ATCC 9945a (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHabib, M.H. / Smith, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01-AI141465 United States
Citation
Journal: Front Microbiol / Year: 2024
Title: Polymerization potential of a bacterial CotA-laccase for beta-naphthol: enzyme structure and comprehensive polymer characterization.
Authors: Refaat, M. / ElRakaiby, M.T. / El Hariri El Nokab, M. / Es Sayed, J. / Elshewy, A. / Sebakhy, K.O. / Moneib, N. / Wang, T. / Smith, T.J. / Habib, M.H.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spore coat protein A
B: Spore coat protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,67333
Polymers122,9552
Non-polymers2,71831
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-382 kcal/mol
Surface area39950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.800, 94.800, 271.658
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Spore coat protein A


Mass: 61477.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus paralicheniformis ATCC 9945a (bacteria)
Gene: B4121_2419 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N2GR66
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2 M ammonium sulfate as the reservoir and the drop was composed of a 3:1 ratio of protein (5 mg mL-1): reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5406 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Oct 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.7→33.2 Å / Num. obs: 36830 / % possible obs: 97.67 % / Redundancy: 3.75 % / Biso Wilson estimate: 22.45 Å2 / Rsym value: 0.112 / Net I/σ(I): 9.1
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 3808

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5134refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→23.7 Å / SU ML: 0.2608 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2322 1846 5.01 %
Rwork0.1894 34984 -
obs0.1915 36830 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.47 Å2
Refinement stepCycle: LAST / Resolution: 2.7→23.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8180 0 123 555 8858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218518
X-RAY DIFFRACTIONf_angle_d0.513911600
X-RAY DIFFRACTIONf_chiral_restr0.04361222
X-RAY DIFFRACTIONf_plane_restr0.00491498
X-RAY DIFFRACTIONf_dihedral_angle_d14.28363168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.311400.24592612X-RAY DIFFRACTION95.89
2.77-2.850.28941340.22822701X-RAY DIFFRACTION97.42
2.85-2.950.26511480.22422689X-RAY DIFFRACTION97.86
2.95-3.050.27021460.20962709X-RAY DIFFRACTION98.18
3.05-3.170.25151390.19982717X-RAY DIFFRACTION99.03
3.17-3.320.19411410.19752707X-RAY DIFFRACTION98.99
3.32-3.490.23271500.19342738X-RAY DIFFRACTION98.77
3.49-3.710.21541400.17922668X-RAY DIFFRACTION97.94
3.71-3.990.23571420.16992722X-RAY DIFFRACTION98.08
3.99-4.390.18651440.15762700X-RAY DIFFRACTION98.17
4.39-5.020.20031450.15422711X-RAY DIFFRACTION97.67
5.03-6.310.23281420.18052679X-RAY DIFFRACTION97.14
6.31-23.70.2571350.21732631X-RAY DIFFRACTION94.56

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