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- PDB-3keb: Thiol peroxidase from Chromobacterium violaceum -

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Basic information

Entry
Database: PDB / ID: 3keb
TitleThiol peroxidase from Chromobacterium violaceum
ComponentsProbable thiol peroxidase
KeywordsOXIDOREDUCTASE / structural genomics / APC40679 / thiol peroxidase. / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Peroxidase
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity
Similarity search - Function
: / Redoxin / Redoxin / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable thiol peroxidase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOsipiuk, J. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of thiol peroxidase from Chromobacterium violaceum
Authors: Osipiuk, J. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionOct 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable thiol peroxidase
B: Probable thiol peroxidase
C: Probable thiol peroxidase
D: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7599
Polymers102,4604
Non-polymers2985
Water13,709761
1
A: Probable thiol peroxidase
B: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3624
Polymers51,2302
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-23 kcal/mol
Surface area15600 Å2
MethodPISA
2
C: Probable thiol peroxidase
D: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3975
Polymers51,2302
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-36 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.630, 59.387, 93.484
Angle α, β, γ (deg.)90.000, 98.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable thiol peroxidase


Mass: 25615.123 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: CV_3708 / Plasmid: pET15b modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7NRS2, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG-3350, 0.2 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→43 Å / Num. all: 74165 / Num. obs: 74165 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.087 / Χ2: 2.218 / Net I/σ(I): 8.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.13 / Num. unique all: 3250 / Χ2: 1.292 / % possible all: 88.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q98

1q98


Resolution: 1.8→43 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.24 / SU B: 6.975 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3740 5 %RANDOM
Rwork0.206 ---
all0.207 74115 --
obs0.207 74115 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.17 Å2 / Biso mean: 18.685 Å2 / Biso min: 2.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20.53 Å2
2---1.04 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5616 0 13 761 6390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226083
X-RAY DIFFRACTIONr_bond_other_d0.0010.024175
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9728331
X-RAY DIFFRACTIONr_angle_other_deg0.978310185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10123.312311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.805151057
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5391554
X-RAY DIFFRACTIONr_chiral_restr0.110.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021299
X-RAY DIFFRACTIONr_mcbond_it1.1151.53623
X-RAY DIFFRACTIONr_mcbond_other0.3941.51435
X-RAY DIFFRACTIONr_mcangle_it1.89425914
X-RAY DIFFRACTIONr_scbond_it3.08532460
X-RAY DIFFRACTIONr_scangle_it4.7454.52368
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 231 -
Rwork0.382 4307 -
all-4538 -
obs-4538 82.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83170.2110.3121.2781-0.18141.1665-0.02990.00650.0012-0.07420.01040.0273-0.0263-0.03960.01950.01550.0109-0.00660.0148-0.0090.009339.040231.631455.5421
20.9782-0.1307-0.52191.4989-0.17440.9522-0.002-0.0041-0.01450.0912-0.03320.075-0.0048-0.00950.03520.0177-0.01210.00790.0108-0.00710.009934.493328.193486.0226
30.92220.0301-0.44391.4840.04850.83410.00940.0082-0.0035-0.0451-0.0368-0.0733-0.00920.00430.02740.01270.01170.00630.01210.00610.011357.229757.981452.9132
40.859-0.19250.32611.1960.18191.0483-0.0308-0.01830.00530.07050.008-0.0269-0.01710.04420.02280.0211-0.0112-0.00470.01530.00780.00752.773461.333583.4339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 176
2X-RAY DIFFRACTION1A223 - 753
3X-RAY DIFFRACTION2B1 - 174
4X-RAY DIFFRACTION2B301 - 303
5X-RAY DIFFRACTION2B223 - 757
6X-RAY DIFFRACTION3C1 - 174
7X-RAY DIFFRACTION3C302 - 305
8X-RAY DIFFRACTION3C223 - 761
9X-RAY DIFFRACTION4D2 - 176
10X-RAY DIFFRACTION4D304
11X-RAY DIFFRACTION4D223 - 760

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