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- PDB-3vec: Rhodococcus jostii RHA1 DypB D153A variant in complex with heme -

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Basic information

Entry
Database: PDB / ID: 3vec
TitleRhodococcus jostii RHA1 DypB D153A variant in complex with heme
ComponentsDypB
KeywordsOXIDOREDUCTASE / peroxidase / lignan / Dyp
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGrigg, J.C. / Singh, R. / Armstrong, Z. / Eltis, L.D. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Distal heme pocket residues of B-type dye-decolorizing peroxidase: arginine but not aspartate is essential for peroxidase activity.
Authors: Singh, R. / Grigg, J.C. / Armstrong, Z. / Murphy, M.E. / Eltis, L.D.
History
DepositionJan 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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_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: DypB
B: DypB
C: DypB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,63513
Polymers112,4813
Non-polymers2,15410
Water5,098283
1
A: DypB
B: DypB
C: DypB
hetero molecules

A: DypB
B: DypB
C: DypB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,27026
Polymers224,9616
Non-polymers4,30920
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area27890 Å2
ΔGint-346 kcal/mol
Surface area63000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.432, 132.432, 160.603
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DypB


Mass: 37493.559 Da / Num. of mol.: 3 / Mutation: D153A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (bacteria) / Strain: RHA1 / Gene: dypB, RHA1_ro02407 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q0SE24, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate trihydrate, 3 M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97952 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 15, 2010
Details: Collimating Mirror with two stripes (Si, Rh/Pt), Toroidal Focusing Mirror (Rh/Pt)
RadiationMonochromator: KOHZU double crystal monochromator (DCM), featuring indirectly water-cooled first crystal and flat, long second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 50195 / % possible obs: 99.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.062 / Χ2: 0.975 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.644.70.54324761.0131100
2.64-2.694.80.46924941.056199.9
2.69-2.744.90.39524961.02199.9
2.74-2.850.31624911.031199.9
2.8-2.8650.28525110.989199.9
2.86-2.935.10.24524901.009199.7
2.93-35.10.19825030.999199.8
3-3.085.10.18125221.055199.8
3.08-3.175.10.14324720.978199.7
3.17-3.285.10.11625330.971199.8
3.28-3.395.10.124910.968199.6
3.39-3.535.10.08325330.902199.6
3.53-3.695.10.06725220.857199.4
3.69-3.885.10.05424810.883199.2
3.88-4.135.10.04325150.763198.6
4.13-4.455.10.03425150.937198.7
4.45-4.895.10.02925131.058198.5
4.89-5.65.10.02725380.943198.2
5.6-7.0550.02525431.047198.3
7.05-504.70.0225561.042193.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefmac_5.6.0117refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QNR

3qnr


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 7.65 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 2552 5.1 %RANDOM
Rwork0.1659 ---
obs0.1682 50106 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.65 Å2 / Biso mean: 51.6314 Å2 / Biso min: 13.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0.38 Å20 Å2
2---0.75 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 141 283 7434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197463
X-RAY DIFFRACTIONr_angle_refined_deg2.3611.98910221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5085951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.41423.871341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.701151111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3551555
X-RAY DIFFRACTIONr_chiral_restr0.1070.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215877
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 209 -
Rwork0.291 3253 -
all-3462 -
obs--99.91 %

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