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- PDB-1of0: CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 1H SOAKING WITH ABTS -

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Basic information

Entry
Database: PDB / ID: 1of0
TitleCRYSTAL STRUCTURE OF BACILLUS SUBTILIS COTA AFTER 1H SOAKING WITH ABTS
ComponentsSPORE COAT PROTEIN A
KeywordsOXIDOREDUCTASE / OXIDASE / LACCASE / ENDOSPORE COAT / REACTION CYCLE / SPORULATION / COPPER-DEPENDENT
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
CU-O LINKAGE / COPPER (I) ION / Chem-EBS / OXYGEN MOLECULE / Laccase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsEnguita, F.J. / Marcal, D. / Grenha, R. / Martins, L.O. / Henriques, A.O. / Carrondo, M.A.
CitationJournal: To be Published
Title: Structural Characterization of a Bacterial Laccase Reaction Cycle
Authors: Enguita, F.J. / Marcal, D. / Grenha, R. / Martins, L.O. / Henriques, A.O. / Carrondo, M.A.
History
DepositionApr 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPORE COAT PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5769
Polymers58,5751
Non-polymers1,0018
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.278, 102.278, 136.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SPORE COAT PROTEIN A / COTA


Mass: 58574.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07788

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Non-polymers , 6 types, 246 molecules

#2: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-C1O / CU-O LINKAGE / Copper(II) oxide


Mass: 79.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CuO
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EBS / 3-ETHYL-2-[(2Z)-2-(3-ETHYL-6-SULFO-1,3-BENZOTHIAZOL-2(3H)-YLIDENE)HYDRAZINO]-6-SULFO-3H-1,3-BENZOTHIAZOL-1-IUM / ABTS


Mass: 514.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N4O6S4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsINVOLVED IN BROWN PIGMENTATION DURING SPOROGENESIS

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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: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growpH: 6 / Details: pH 6.00

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8459
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8459 Å / Relative weight: 1
ReflectionResolution: 2.45→19.14 Å / Num. obs: 30797 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 5.9
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 1.95 / % possible all: 93.8

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Processing

Software
NameClassification
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSK

1gsk


Resolution: 2.45→100 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: COMPLETENESS FOR
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1530 5 %RANDOM
Rwork0.197 ---
obs0.197 30797 --
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å24 Å20 Å2
2--1.99 Å20 Å2
3----4.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.45→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 51 238 4334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 261 5.1 %
Rwork0.232 4812 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ABT.PARAMABT.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5GOL.PARAMGOL.TOP

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