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- PDB-4ep6: Crystal structure of the XplA heme domain in complex with imidazo... -

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Basic information

Entry
Database: PDB / ID: 4ep6
TitleCrystal structure of the XplA heme domain in complex with imidazole and PEG
ComponentsCytochrome P450-like protein XplA
KeywordsOXIDOREDUCTASE / P450 enzyme / P450 monoxygenase / explosive RDX
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / FMN binding / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 ...Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Cytochrome P450-like protein XplA
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBui, S.H. / McLean, K.J. / Cheesman, M.R. / Bradley, J.M. / Rigby, S.E.J. / Leys, D. / Munro, A.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Unusual Spectroscopic and Ligand Binding Properties of the Cytochrome P450-Flavodoxin Fusion Enzyme XplA.
Authors: Bui, S.H. / McLean, K.J. / Cheesman, M.R. / Bradley, J.M. / Rigby, S.E. / Levy, C.W. / Leys, D. / Munro, A.W.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Cytochrome P450-like protein XplA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3184
Polymers43,3941
Non-polymers9243
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.120, 136.120, 75.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Cytochrome P450-like protein XplA


Mass: 43393.867 Da / Num. of mol.: 1 / Fragment: heme domain (UNP residues 161-552)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: xplA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GPH7, Oxidoreductases
#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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 4.01 Å3/Da / Density % sol: 69.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM magnesium chloride, 0.1 M imidazole/MES, pH 6.5, 30% PEG550 MME, PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→43.04 Å / Num. all: 28983 / Num. obs: 28983 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WIV

2wiv


Resolution: 2.3→43.04 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.152 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24179 1534 5 %RANDOM
Rwork0.20089 ---
all0.20297 28983 --
obs0.20297 28983 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.021 Å2
Baniso -1Baniso -2Baniso -3
1--3.45 Å20 Å20 Å2
2---3.45 Å2-0 Å2
3---6.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3056 0 64 147 3267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223189
X-RAY DIFFRACTIONr_bond_other_d0.0010.022145
X-RAY DIFFRACTIONr_angle_refined_deg1.8852.0044358
X-RAY DIFFRACTIONr_angle_other_deg1.07735177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8275393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.6923.2150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19215475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7891530
X-RAY DIFFRACTIONr_chiral_restr0.110.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02661
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9141.51967
X-RAY DIFFRACTIONr_mcbond_other0.2131.5780
X-RAY DIFFRACTIONr_mcangle_it1.71623169
X-RAY DIFFRACTIONr_scbond_it2.88431222
X-RAY DIFFRACTIONr_scangle_it4.5884.51188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 103 -
Rwork0.28 2142 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 6.526 Å / Origin y: 19.565 Å / Origin z: 1.986 Å
111213212223313233
T0.005 Å20.0012 Å20.0022 Å2-0.0172 Å20.0045 Å2--0.1173 Å2
L0.7424 °2-0.1036 °20.0641 °2-1.2943 °20.1162 °2--0.3391 °2
S0.0096 Å °0.0466 Å °0.2053 Å °-0.071 Å °-0.0246 Å °-0.0865 Å °0.0165 Å °-0.0574 Å °0.015 Å °

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