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- PDB-3fob: Crystal structure of bromoperoxidase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 3fob
TitleCrystal structure of bromoperoxidase from Bacillus anthracis
ComponentsBromoperoxidaseBromide peroxidase
KeywordsOXIDOREDUCTASE / structural genomics / IDP00046 / Bromoperoxidase / Bacillus anthracis / Peroxidase / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


bromide peroxidase activity / chloride peroxidase / chloride peroxidase activity / response to toxic substance
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha/beta hydrolase / Bromoperoxidase
Similarity search - Component
Biological speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsOsipiuk, J. / Gu, M. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of bromoperoxidase from Bacillus anthracis.
Authors: Osipiuk, J. / Gu, M. / Stam, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionDec 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr2_auth_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromoperoxidase
B: Bromoperoxidase
C: Bromoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8868
Polymers93,7343
Non-polymers1525
Water13,025723
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-11.3 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.037, 48.326, 101.932
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number4
Space group name H-MP1211
DetailsACCORDING TO AUTHORS, THE BIOLOGICAL UNIT ASSEMBLY THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein Bromoperoxidase / Bromide peroxidase


Mass: 31244.584 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Strain: Ames / Gene: BAS2941, BA_3165, GBAA3165 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81NM3, UniProt: A0A6L8NUA5*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride, 0.1 M Hepes buffer, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 2, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.74→28.4 Å / Num. all: 76114 / Num. obs: 76114 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 27.405
Reflection shellResolution: 1.74→1.78 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.56 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BRO

1bro


Resolution: 1.74→27.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.303 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19484 3809 5 %RANDOM
Rwork0.16362 ---
obs0.16524 75908 98.92 %-
all-75908 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.094 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.61 Å2
2--0.37 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.74→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6524 0 5 723 7252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226885
X-RAY DIFFRACTIONr_bond_other_d0.0010.024629
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9549393
X-RAY DIFFRACTIONr_angle_other_deg0.977311309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8885883
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05324.401334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.673151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5981532
X-RAY DIFFRACTIONr_chiral_restr0.1080.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217845
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021451
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_it0.9651.54207
X-RAY DIFFRACTIONr_mcbond_other0.3381.51727
X-RAY DIFFRACTIONr_mcangle_it1.60726797
X-RAY DIFFRACTIONr_scbond_it2.7132678
X-RAY DIFFRACTIONr_scangle_it4.1924.52570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 275 -
Rwork0.225 4977 -
obs--92.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6510.09890.0380.4899-0.05850.84660.01580.0097-0.00840.0313-0.01220.0220.06190.0325-0.00360.03860.0085-0.00470.007-0.00410.003412.2951-24.0709100.2243
21.0020.15-0.09910.3730.13490.93640.02710.06440.07010.0157-0.00450.01650.01290.0973-0.02270.0138-0.0002-0.00620.02350.0080.014726.1528-12.851966.735
30.44890.131-0.09180.53390.04580.8451-0.03420.0430.07230.02480.01760.1182-0.0007-0.13980.01650.0211-0.0039-0.01350.02640.00650.0496-9.4916-24.997769.4002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 278
2X-RAY DIFFRACTION2B-2 - 278
3X-RAY DIFFRACTION3C2 - 278

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