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- PDB-1a8s: CHLOROPEROXIDASE F/PROPIONATE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a8s
TitleCHLOROPEROXIDASE F/PROPIONATE COMPLEX
ComponentsCHLOROPEROXIDASE F
KeywordsHALOPEROXIDASE / OXIDOREDUCTASE / PROPIONATE COMPLEX
Function / homology
Function and homology information


chloride peroxidase / chloride 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
PROPANOIC ACID / Non-heme chloroperoxidase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHLOROPEROXIDASE F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0116
Polymers29,5531
Non-polymers4585
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CHLOROPEROXIDASE F
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)360,13872
Polymers354,63812
Non-polymers5,50060
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area31680 Å2
ΔGint-758 kcal/mol
Surface area106890 Å2
MethodPISA
3
A: CHLOROPEROXIDASE F
hetero molecules

A: CHLOROPEROXIDASE F
hetero molecules

A: CHLOROPEROXIDASE F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,03418
Polymers88,6593
Non-polymers1,37515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
MethodPQS
Unit cell
Length a, b, c (Å)106.470, 106.470, 106.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein CHLOROPEROXIDASE F / HALOPEROXIDASE F


Mass: 29553.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: BL914 / Gene: CPOF / Plasmid: PSK12 / Gene (production host): CPOF / Production host: Escherichia coli (E. coli) / References: UniProt: O31158, chloride peroxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 3.36 Å3/Da / Density % sol: 63.1 %
Crystal growpH: 6.6
Details: 1.0 M AMMONIUM SULFATE 50MM CITRATE/PHOSPHATE BUFFER PH 6.6
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMcitrate-phosphate1reservoir
2100 mMsodium propionate1reservoir

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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: Oct 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: 1.8→35.5 Å / Num. obs: 33363 / % possible obs: 88.9 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 18.38 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 4.9 / % possible all: 80.7
Reflection shell
*PLUS
% possible obs: 80.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
REFMACrefinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED COORDINATES OF CHLOROPEROXIDASE L

Resolution: 1.8→70 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1668 5 %RANDOM
Rwork0.176 ---
obs0.173 33363 88.9 %-
Displacement parametersBiso mean: 20.57 Å2
Refine analyzeLuzzati d res low obs: 8.4 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 25 335 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.522
X-RAY DIFFRACTIONp_mcangle_it1.883
X-RAY DIFFRACTIONp_scbond_it2.052
X-RAY DIFFRACTIONp_scangle_it2.923
X-RAY DIFFRACTIONp_plane_restr0.0240.02
X-RAY DIFFRACTIONp_chiral_restr0.1540.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.1950.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor14.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor33.820
X-RAY DIFFRACTIONp_special_tor015

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