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- PDB-1brt: BROMOPEROXIDASE A2 MUTANT M99T -

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Basic information

Entry
Database: PDB / ID: 1brt
TitleBROMOPEROXIDASE A2 MUTANT M99T
ComponentsBROMOPEROXIDASE A2
KeywordsHALOPEROXIDASE / OXIDOREDUCTASE / PEROXIDASE / ALPHA/BETA HYDROLASE FOLD / MUTANT M99T
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-haem bromoperoxidase BPO-A2
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 30, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BROMOPEROXIDASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2842
Polymers30,2481
Non-polymers351
Water4,432246
1
A: BROMOPEROXIDASE A2
hetero molecules

A: BROMOPEROXIDASE A2
hetero molecules

A: BROMOPEROXIDASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8516
Polymers90,7453
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
Unit cell
Length a, b, c (Å)121.720, 121.720, 121.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 30248.328 Da / Num. of mol.: 1 / Mutation: M99T
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, chloride peroxidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.49 Å3/Da / Density % sol: 50.5 %
Crystal growpH: 8.5 / Details: 1.8 M AMMONIUM SULFATE 0.1 M TRIS/HCL, PH 8.5.
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium sulfate1reservoir
20.1 MTris-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: Mar 1, 1995 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→27.2 Å / Num. obs: 45113 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.5
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 12 / % possible all: 84.7
Reflection shell
*PLUS
% possible obs: 84.7 %

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Processing

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

1bro


Resolution: 1.5→90 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.164 2283 5 %RANDOM
Rwork0.147 ---
obs0.14 45133 94.1 %-
Displacement parametersBiso mean: 15.22 Å2
Refine analyzeLuzzati d res low obs: 8.8 Å / Luzzati sigma a obs: 0.02 Å
Refinement stepCycle: LAST / Resolution: 1.5→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 1 246 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.552
X-RAY DIFFRACTIONp_mcangle_it2.243
X-RAY DIFFRACTIONp_scbond_it2.842
X-RAY DIFFRACTIONp_scangle_it43
X-RAY DIFFRACTIONp_plane_restr0.0250.02
X-RAY DIFFRACTIONp_chiral_restr0.1710.15
X-RAY DIFFRACTIONp_singtor_nbd0.1650.3
X-RAY DIFFRACTIONp_multtor_nbd0.2620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1430.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor14.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.220
X-RAY DIFFRACTIONp_special_tor

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