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- PDB-5zll: Mutation in the trinuclear site of CotA-laccase: H493C mutant, PH 8.0 -

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Basic information

Entry
Database: PDB / ID: 5zll
TitleMutation in the trinuclear site of CotA-laccase: H493C mutant, PH 8.0
ComponentsSpore coat protein A
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


bilirubin oxidase / laccase / sporulation resulting in formation of a cellular spore / outer membrane-bounded periplasmic space / 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 / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Laccase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsXie, T. / Liu, Z.C. / Wang, G.G.
CitationJournal: Chembiochem / Year: 2018
Title: Structural Insight into the Allosteric Coupling of Cu1 Site and Trinuclear Cu Cluster in CotA Laccase.
Authors: Xie, T. / Liu, Z. / Wang, G.
History
DepositionMar 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spore coat protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0719
Polymers58,5401
Non-polymers5318
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-26 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.827, 101.827, 135.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Spore coat protein A


Mass: 58539.789 Da / Num. of mol.: 1 / Mutation: H493C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: cotA, pig, BSU06300 / Production host: Escherichia coli (E. coli) / References: UniProt: P07788
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30-42%(v/v) ethylene glycol, 100mM NaCl, 25mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→29.9 Å / Num. obs: 25463 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 11.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gsk

1gsk


Resolution: 2.6→29.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.253 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21529 1296 5.1 %RANDOM
Rwork0.16993 ---
obs0.1723 24146 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.04 Å20 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.6→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 25 250 4328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194194
X-RAY DIFFRACTIONr_bond_other_d0.0010.023890
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9615712
X-RAY DIFFRACTIONr_angle_other_deg0.80138985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2565500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86823.663202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47215664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1561528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214701
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02961
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3353.1112009
X-RAY DIFFRACTIONr_mcbond_other2.3353.1092008
X-RAY DIFFRACTIONr_mcangle_it3.7044.6512506
X-RAY DIFFRACTIONr_mcangle_other3.7044.6532507
X-RAY DIFFRACTIONr_scbond_it2.4743.3632185
X-RAY DIFFRACTIONr_scbond_other2.4713.3632185
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.974.9383207
X-RAY DIFFRACTIONr_long_range_B_refined5.8424.7524833
X-RAY DIFFRACTIONr_long_range_B_other5.77724.6574737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 97 -
Rwork0.235 1748 -
obs--99.62 %

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