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- PDB-5hdi: Structural characterization of CYP144A1, a Mycobacterium tubercul... -

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Basic information

Entry
Database: PDB / ID: 5hdi
TitleStructural characterization of CYP144A1, a Mycobacterium tuberculosis cytochrome P450
ComponentsCytochrome P450 144
KeywordsOXIDOREDUCTASE / monooxygenase / cytochrome P450 / heme-binding
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / peptidoglycan-based cell wall / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 144
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsChenge, J. / Driscoll, M.D. / McLean, K.J. / Munro, A.W. / Leys, D.
CitationJournal: Sci Rep / Year: 2016
Title: Structural characterization of CYP144A1 - a cytochrome P450 enzyme expressed from alternative transcripts in Mycobacterium tuberculosis.
Authors: Chenge, J. / Kavanagh, M.E. / Driscoll, M.D. / McLean, K.J. / Young, D.B. / Cortes, T. / Matak-Vinkovic, D. / Levy, C.W. / Rigby, S.E. / Leys, D. / Abell, C. / Munro, A.W.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 144
B: Cytochrome P450 144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2754
Polymers88,0422
Non-polymers1,2332
Water9,836546
1
A: Cytochrome P450 144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6382
Polymers44,0211
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome P450 144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6382
Polymers44,0211
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.350, 117.790, 122.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450 144


Mass: 44021.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cyp144, Rv1777, MTCY25C11.04 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPL1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Crystallography was performed using the sitting drop method using 20 mg/ml CYP144A1. Drops were prepared by the addition of 0.2 microl of CYP144A1-FLV and -TRV proteins to 0.2 microl of ...Details: Crystallography was performed using the sitting drop method using 20 mg/ml CYP144A1. Drops were prepared by the addition of 0.2 microl of CYP144A1-FLV and -TRV proteins to 0.2 microl of mother liquor and by incubating at 4 oC. Following initial crystallogenesis using commercial screens, crystallization conditions were further refined to 0.8 or 1.0 M (NH4)2SO4 with 0.1 M HEPES, pH 7.55, and 25% PEG 3350. Single crystals were flash cooled after addition of 10% PEG 200 as cryoprotectant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→88.58 Å / Num. obs: 116903 / % possible obs: 98.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 10.4
Reflection shellResolution: 1.54→1.58 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 2.3 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XKR

2xkr


Resolution: 1.54→84.77 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.32 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19238 6118 5 %RANDOM
Rwork0.13761 ---
obs0.14028 116903 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.554 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å2-0 Å2
2---2.08 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.54→84.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 86 546 6676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196469
X-RAY DIFFRACTIONr_bond_other_d0.0010.026129
X-RAY DIFFRACTIONr_angle_refined_deg1.8721.9768866
X-RAY DIFFRACTIONr_angle_other_deg0.987314016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6725832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21923.149289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.953151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.531558
X-RAY DIFFRACTIONr_chiral_restr0.1260.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217554
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021544
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.629312598
X-RAY DIFFRACTIONr_sphericity_free26.915128
X-RAY DIFFRACTIONr_sphericity_bonded17.578512851
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 441 -
Rwork0.214 8401 -
obs--96.74 %

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