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- PDB-1a88: CHLOROPEROXIDASE L -

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Basic information

Entry
Database: PDB / ID: 1a88
TitleCHLOROPEROXIDASE L
ComponentsCHLOROPEROXIDASE L
KeywordsHALOPEROXIDASE / OXIDOREDUCTASE
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
Non-heme chloroperoxidase
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionApr 3, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
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 L
B: CHLOROPEROXIDASE L
C: CHLOROPEROXIDASE L


Theoretical massNumber of molelcules
Total (without water)89,4493
Polymers89,4493
Non-polymers00
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-22 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.500, 176.500, 64.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.311822, -0.852843, -0.418837), (0.024857, 0.433343, -0.900886), (0.949815, -0.291327, -0.113927)70.96638, 14.80369, -25.69099
2given(-0.312554, 0.020945, 0.949669), (-0.860924, 0.416218, -0.292526), (-0.401396, -0.909024, -0.112059)46.42327, 47.53159, 40.50269

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Components

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


Mass: 29816.207 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Strain: TK64 / Gene: CPO-L / Plasmid: PRB882 / Gene (production host): CPO-L / Production host: Streptomyces aureofaciens (bacteria) / Strain (production host): TUE24-88 / References: UniProt: P49323, chloride peroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.79 Å3/Da / Density % sol: 55.3 %
Crystal growpH: 8.2 / Details: 2.0 M AMMONIUM SULFATE 100MM TRIS/HCL PH 8.2
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1reservoir
2100 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: 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: 1.9→44.2 Å / Num. obs: 65934 / % possible obs: 84.7 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 5.2 / % possible all: 74.4
Reflection
*PLUS
Lowest resolution: 130 Å
Reflection shell
*PLUS
% possible obs: 74.4 %

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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 1A8Q

1a8q


Resolution: 1.9→130 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3325 5 %RANDOM
Rwork0.16 ---
obs0.16 65934 84.7 %-
Displacement parametersBiso mean: 22.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→130 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6315 0 0 507 6822
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.262
X-RAY DIFFRACTIONp_mcangle_it1.783
X-RAY DIFFRACTIONp_scbond_it1.552
X-RAY DIFFRACTIONp_scangle_it3.093
X-RAY DIFFRACTIONp_plane_restr0.0240.02
X-RAY DIFFRACTIONp_chiral_restr0.1350.15
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.2490.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1180.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor16.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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