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- PDB-4yvu: Crystal structure of CotA native enzyme in the acid condition, PH5.6 -

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Basic information

Entry
Database: PDB / ID: 4yvu
TitleCrystal structure of CotA native enzyme in the acid condition, PH5.6
ComponentsSpore coat protein A
KeywordsOXIDOREDUCTASE / Spore coat protein A / laccase
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 / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, Z.C. / Xie, T. / Wang, G.G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of CotA laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site
Authors: Liu, Z. / Xie, T. / Zhong, Q. / Wang, G.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)59,1069
Polymers58,5751
Non-polymers5318
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-27 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.730, 101.730, 135.572
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: 58574.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: cotA, pig, BSU06300 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P07788
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30-42%(v/v) ethylene glycol,100mM sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→29.4 Å / Num. obs: 36605 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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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: 2.3→29.38 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.773 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18693 1824 5 %RANDOM
Rwork0.15899 ---
obs0.16041 34656 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.344 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.1 Å20 Å2
2--0.1 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4080 0 25 405 4510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194232
X-RAY DIFFRACTIONr_bond_other_d0.0010.023927
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.965769
X-RAY DIFFRACTIONr_angle_other_deg0.79139071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2825506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69823.676204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50615668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3711528
X-RAY DIFFRACTIONr_chiral_restr0.0910.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02972
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_it1.5651.9582027
X-RAY DIFFRACTIONr_mcbond_other1.5571.9562026
X-RAY DIFFRACTIONr_mcangle_it2.5422.9272532
X-RAY DIFFRACTIONr_mcangle_other2.5452.9292533
X-RAY DIFFRACTIONr_scbond_it2.0672.1842205
X-RAY DIFFRACTIONr_scbond_other2.0672.1842205
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3643.1813238
X-RAY DIFFRACTIONr_long_range_B_refined5.89516.695090
X-RAY DIFFRACTIONr_long_range_B_other5.49216.1764900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 108 -
Rwork0.185 2473 -
obs--97.32 %

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