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- PDB-1bro: BROMOPEROXIDASE A2 -

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Basic information

Entry
Database: PDB / ID: 1bro
TitleBROMOPEROXIDASE A2
ComponentsBROMOPEROXIDASE A2
KeywordsHALOPEROXIDASE / ANTIBIOTIC BIOSYNTHESIS / OXIDOREDUCTASE / PEROXIDASE / ALPHA/BETA HYDROLASE FOLD
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / antibiotic biosynthetic process / peroxidase activity
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
Non-haem bromoperoxidase BPO-A2
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 2.05 Å
AuthorsHecht, H.J. / Sobek, H. / Haag, T. / Pfeifer, O. / Van Pee, K.H.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: The metal-ion-free oxidoreductase from Streptomyces aureofaciens has an alpha/beta hydrolase fold.
Authors: Hecht, H.J. / Sobek, H. / Haag, T. / Pfeifer, O. / van Pee, K.H.
#1: Journal: Naturally-Produced Organohalogens (in: Environment & Chemistry, V.1)
Year: 1995
Title: Reaction Mechanism and 3-Dimensional Structure of Bacterial Non-Haem Haloperoxidases
Authors: Van Pee, K.H. / Hecht, H.J. / Haag, T. / Pfeifer, O. / Bantleon, R. / Sobek, H. / Pelletier, I. / Altenbuchner, J.
#2: Journal: J.Gen.Microbiol. / Year: 1992
Title: Molecular Cloning and Sequencing of a Non-Haem Bromoperoxidase Gene from Streptomyces Aureofaciens Atcc 10762
Authors: Pfeifer, O. / Pelletier, I. / Altenbuchner, J. / Van Pee, K.H.
History
DepositionJun 1, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BROMOPEROXIDASE A2
B: BROMOPEROXIDASE A2


Theoretical massNumber of molelcules
Total (without water)60,5572
Polymers60,5572
Non-polymers00
Water4,234235
1
A: BROMOPEROXIDASE A2

A: BROMOPEROXIDASE A2

A: BROMOPEROXIDASE A2


Theoretical massNumber of molelcules
Total (without water)90,8353
Polymers90,8353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
2
B: BROMOPEROXIDASE A2

B: BROMOPEROXIDASE A2

B: BROMOPEROXIDASE A2


Theoretical massNumber of molelcules
Total (without water)90,8353
Polymers90,8353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
Unit cell
Length a, b, c (Å)126.500, 126.500, 126.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.33864, 0.72493, 0.59983), (-0.72498, 0.60739, -0.32478), (-0.59977, -0.32488, 0.73125)
Vector: -54.00097, 20.21999, 71.15529)

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Components

#1: Protein BROMOPEROXIDASE A2 / HALOPEROXIDASE A2 / CHLOROPEROXIDASE A2


Mass: 30278.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Gene: BPOA2 / Plasmid: PIJ486 / Gene (production host): BPOA2 / Production host: Streptomyces lividans (bacteria) / Strain (production host): TK64
References: UniProt: P29715, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.8 Å3/Da / Density % sol: 56.2 %
Crystal growpH: 8 / Details: 1.8 M AMMONIUM SULFATE PH 8.0.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
25 mMammonium acetate1drop
31.8 Mammonium sulfate1reservoir
450 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Mar 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.99→44.7 Å / Num. obs: 45014 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 2.05 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.11 / % possible all: 1.99

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Processing

Software
NameVersionClassification
CCP4model building
PROLSQrefinement
XENGENdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 2.05→10 Å / σ(F): 0
Details: CCP4 DISTRIBUTED DICT.DAT FOR PROLSQ. FINAL RMS COORD. SHIFT 0.0120 ANGSTROMS
Num. reflection% reflection
obs41321 98.2 %
Displacement parametersBiso mean: 27.84 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 0 235 4529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0580.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0580.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9991
X-RAY DIFFRACTIONp_mcangle_it1.5951.5
X-RAY DIFFRACTIONp_scbond_it1.5081
X-RAY DIFFRACTIONp_scangle_it2.0571.5
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1740.15
X-RAY DIFFRACTIONp_singtor_nbd0.1830.3
X-RAY DIFFRACTIONp_multtor_nbd0.2670.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1690.3
X-RAY DIFFRACTIONp_planar_tor2.5793
X-RAY DIFFRACTIONp_staggered_tor15.43315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.65720
X-RAY DIFFRACTIONp_special_tor

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