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- PDB-1a8u: CHLOROPEROXIDASE T/BENZOATE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a8u
TitleCHLOROPEROXIDASE T/BENZOATE COMPLEX
ComponentsCHLOROPEROXIDASE T
KeywordsHALOPEROXIDASE / OXIDOREDUCTASE / BENZOATE COMPLEX
Function / homology
Function and homology information


chloride peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
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
BENZOIC ACID / Non-heme chloroperoxidase
Similarity search - Component
Biological speciesStreptomyces aureofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 26, 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 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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: CHLOROPEROXIDASE T
B: CHLOROPEROXIDASE T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2239
Polymers60,4992
Non-polymers7257
Water12,088671
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.870, 124.870, 124.870
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: (0.337597, -0.723701, -0.601901), (0.721281, 0.609746, -0.328578), (0.604799, -0.323213, 0.72784)
Vector: 74.698, 49.798, -12.766)

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Components

#1: Protein CHLOROPEROXIDASE T / BROMOPEROXIDASE T


Mass: 30249.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH BENZOIC ACID / Source: (gene. exp.) Streptomyces aureofaciens (bacteria) / Strain: TUE24 / Gene: CPOT / Plasmid: PIJ486 / Gene (production host): CPOT / Production host: Streptomyces lividans (bacteria) / Strain (production host): TK64 / References: UniProt: O31168, chloride peroxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.65 Å3/Da / Density % sol: 56.2 %
Crystal growpH: 7.8
Details: 1.8 M AMMONIUM SULFATE PH 7.8., SMALL AMOUNTS OF SOLID SODIUM BENZOATE
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium sulfate1reservoir
250 mMTris-HCl1reservoir
410 mMpotassium bromide1reservoir
3sodium benzoate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 / 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→28 Å / Num. obs: 84499 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 13.49 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 20
Reflection shellResolution: 1.6→1.67 Å / Redundancy: 4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 9 / % possible all: 97.9
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A7U

1a7u


Resolution: 1.6→90 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.171 4229 5 %RANDOM
Rwork0.152 ---
obs0.149 84499 98.9 %-
Displacement parametersBiso mean: 13.25 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.02 Å
Refinement stepCycle: LAST / Resolution: 1.6→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 25 671 4986
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.072
X-RAY DIFFRACTIONp_mcangle_it1.573
X-RAY DIFFRACTIONp_scbond_it1.692
X-RAY DIFFRACTIONp_scangle_it1.423
X-RAY DIFFRACTIONp_plane_restr0.0220.02
X-RAY DIFFRACTIONp_chiral_restr0.1310.15
X-RAY DIFFRACTIONp_singtor_nbd0.1690.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.0930.3
X-RAY DIFFRACTIONp_planar_tor4.17
X-RAY DIFFRACTIONp_staggered_tor11.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.420
X-RAY DIFFRACTIONp_special_tor015

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