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- PDB-8e5j: The crystal structure of 4-n-butylbenzoic acid bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 8e5j
TitleThe crystal structure of 4-n-butylbenzoic acid bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450 / Heme
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
4-butylbenzoic acid / Mesoheme / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDoherty, D.Z. / Bell, S.G. / Bruning, J.B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: Chem Asian J / Year: 2022
Title: Exploring the Factors which Result in Cytochrome P450 Catalyzed Desaturation Versus Hydroxylation.
Authors: Coleman, T. / Doherty, D.Z. / Zhang, T. / Podgorski, M.N. / Qiao, R. / Lee, J.H.Z. / Bruning, J.B. / De Voss, J.J. / Zhou, W. / Bell, S.G.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 2.0Mar 13, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7334
Polymers42,8991
Non-polymers8343
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.010, 51.540, 79.310
Angle α, β, γ (deg.)90.000, 91.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 42898.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2IU02
#2: Chemical ChemComp-MH0 / Mesoheme


Mass: 620.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HX1 / 4-butylbenzoic acid


Mass: 178.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion
Details: 0.2 M magnesium acetate, 15-30% w/v PEG3350, 0.1 M Bis-Tris, pH 5-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→43.21 Å / Num. obs: 16355 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.29 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.105 / Rrim(I) all: 0.276 / Net I/σ(I): 7.2 / Num. measured all: 109842 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.386.81.0011081115950.7450.4111.0832.599.9
8.91-43.215.70.0817343040.9910.0350.08817.699.3

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UVB

5uvb


Resolution: 2.3→43.209 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 867 5.3 %
Rwork0.1665 15477 -
obs0.1694 16344 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.36 Å2 / Biso mean: 25.7239 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: final / Resolution: 2.3→43.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 57 191 3269
Biso mean--20.32 29.49 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043168
X-RAY DIFFRACTIONf_angle_d0.6874327
X-RAY DIFFRACTIONf_chiral_restr0.043470
X-RAY DIFFRACTIONf_plane_restr0.005574
X-RAY DIFFRACTIONf_dihedral_angle_d10.0482607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3003-2.44440.28391360.21242581
2.4444-2.63310.31461300.20362564
2.6331-2.8980.26211510.1952539
2.898-3.31720.2281510.16762561
3.3172-4.17880.19051450.13732593
4.1788-43.2090.17871540.1482639

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