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- PDB-3qns: DyPB from Rhodococcus jostii RHA1, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 3qns
TitleDyPB from Rhodococcus jostii RHA1, crystal form 2
ComponentsDyP Peroxidase
KeywordsOXIDOREDUCTASE / peroxidase / lignan / heme / DyP / enzyme
Function / homology
Function and homology information


peroxidase activity / heme binding / metal ion binding / cytosol
Similarity search - Function
: / : / Dyp-type peroxidase, C-terminal / Dyp-type peroxidase, N-terminal / DyP-type peroxidase family. / Dyp-type peroxidase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Iron-dependent peroxidase
Similarity search - Component
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsGrigg, J.C. / Roberts, J.N. / Singh, R. / Eltis, L.D. / Murphy, M.E.P.
CitationJournal: Biochemistry / Year: 2011
Title: Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1.
Authors: Roberts, J.N. / Singh, R. / Grigg, J.C. / Murphy, M.E. / Bugg, T.D. / Eltis, L.D.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DyP Peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8079
Polymers37,5381
Non-polymers1,2698
Water7,422412
1
A: DyP Peroxidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)232,84054
Polymers225,2256
Non-polymers7,61448
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation16_454y-2/3,x+2/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area35390 Å2
ΔGint-424 kcal/mol
Surface area62930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.699, 127.699, 178.242
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

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Components

#1: Protein DyP Peroxidase


Mass: 37537.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Strain: RHA1 / Gene: DyPB, RHA1_ro02407 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q0SE24
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 3.73 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.26 M ammonium sulfate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2010 / Details: Rh coated flat mirror
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→93.972 Å / Num. all: 108171 / Num. obs: 108171 / % possible obs: 98.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.485.30.387281293152430.38796.2
1.48-1.575.40.2592.978989147270.25998.1
1.57-1.675.60.1764.378816140200.17699.3
1.67-1.8160.1345.479348131320.13499.9
1.81-1.986.60.0927.579727121490.092100
1.98-2.216.80.05911.274991110120.059100
2.21-2.566.80.04514.26622197180.045100
2.56-3.136.40.04612.95292082460.04699.8
3.13-4.436.70.02722.74276063790.02799.4
4.43-33.9297.10.01931.32519735450.01997.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.61 Å33.93 Å
Translation1.61 Å33.93 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-IceIcedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→33.93 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.09 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1475 5407 5 %RANDOM
Rwork0.1301 ---
obs0.131 108165 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 180.43 Å2 / Biso mean: 17.2251 Å2 / Biso min: 6.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.21 Å20 Å2
2--0.43 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 83 412 2851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212697
X-RAY DIFFRACTIONr_angle_refined_deg1.422.0243711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.99524.065123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.28115399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0431520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212144
X-RAY DIFFRACTIONr_mcbond_it1.3791.51679
X-RAY DIFFRACTIONr_mcangle_it2.23722728
X-RAY DIFFRACTIONr_scbond_it3.14231018
X-RAY DIFFRACTIONr_scangle_it4.4584.5983
X-RAY DIFFRACTIONr_rigid_bond_restr1.39132697
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 365 -
Rwork0.218 7341 -
all-7706 -
obs--95.57 %

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