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- PDB-1a8q: BROMOPEROXIDASE A1 -

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Basic information

Entry
Database: PDB / ID: 1a8q
TitleBROMOPEROXIDASE A1
ComponentsBROMOPEROXIDASE A1
KeywordsHALOPEROXIDASE / OXIDOREDUCTASE
Function / homology
Function and homology information


antibiotic biosynthetic process / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / 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-heme chloroperoxidase CPO-A1
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHofmann, B. / Toelzer, S. / Pelletier, I. / Altenbuchner, J. / Van Pee, K.-H. / Hecht, H.-J.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Structural investigation of the cofactor-free chloroperoxidases.
Authors: Hofmann, B. / Tolzer, S. / Pelletier, I. / Altenbuchner, J. / van Pee, K.H. / Hecht, H.J.
History
DepositionMar 27, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BROMOPEROXIDASE A1


Theoretical massNumber of molelcules
Total (without water)30,3821
Polymers30,3821
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BROMOPEROXIDASE A1

A: BROMOPEROXIDASE A1

A: BROMOPEROXIDASE A1


Theoretical massNumber of molelcules
Total (without water)91,1463
Polymers91,1463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5150 Å2
ΔGint-35 kcal/mol
Surface area27740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.770, 80.770, 91.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein BROMOPEROXIDASE A1 / CHLOROPEROXIDASE A1 / HALOPEROXIDASE A1


Mass: 30381.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Gene: BPOA1 / Plasmid: PIJ486 / Gene (production host): BPOA1 / Production host: Streptomyces lividans (bacteria) / Strain (production host): TK64 / References: UniProt: P33912, chloride peroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.85 Å3/Da / Density % sol: 57 %
Crystal growpH: 8 / Details: 2.0 M AMMONIUM SULFATE 50MM TRIS/HCL PH 8.0
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulfate1reservoir
250 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.75→23 Å / Num. obs: 31158 / % possible obs: 90.8 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 14.25 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.8
Reflection shellResolution: 1.75→1.83 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 10.4 / % possible all: 90.6
Reflection shell
*PLUS
% possible obs: 90.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRO

1bro


Resolution: 1.75→70 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1566 5 %RANDOM
Rwork0.169 ---
obs0.158 31158 90.8 %-
Displacement parametersBiso mean: 15.02 Å2
Refine analyzeLuzzati d res low obs: 9 Å / Luzzati sigma a obs: 0.06 Å
Refinement stepCycle: LAST / Resolution: 1.75→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 0 207 2350
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.412
X-RAY DIFFRACTIONp_mcangle_it2.033
X-RAY DIFFRACTIONp_scbond_it2.22
X-RAY DIFFRACTIONp_scangle_it3.413
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.1370.15
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1350.3
X-RAY DIFFRACTIONp_planar_tor4.37
X-RAY DIFFRACTIONp_staggered_tor14.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.820
X-RAY DIFFRACTIONp_special_tor015

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