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- PDB-5u6w: The crystal structure of 4-methylaminobenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 5u6w
TitleThe crystal structure of 4-methylaminobenzoate-bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450 / Substrate
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 / 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
4-(methylamino)benzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.644 Å
AuthorsColeman, T. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: Acs Catalysis / Year: 2018
Title: Cytochrome P450 CYP199A4 from Rhodopseudomonas palustris Catalyzes Heteroatom Dealkylations, Sulfoxidation, and Amide and Cyclic Hemiacetal Formation
Authors: Coleman, T. / Wong, S.H. / Podgorski, M.N. / Bruning, J.B. / De Voss, J.J. / Bell, S.G.
History
DepositionDec 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,7024
Polymers42,8991
Non-polymers8033
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.365, 51.152, 78.920
Angle α, β, γ (deg.)90.000, 91.980, 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 / Fragment: UNP residues 18-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain HaA2) (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2IU02
#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-81P / 4-(methylamino)benzoic acid


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2
#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.: 85 / 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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M MgAc Bis-Tris 0.1M, pH 5.5 PEG 3350, 23 % w/v. 1mM 4-methylaminobenzoic acid in protein sample.
PH range: 5-5.75 / Temp details: 16 C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.63→44.34 Å / Num. obs: 10517 / % possible obs: 98.6 % / Redundancy: 7.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.099 / Rrim(I) all: 0.269 / Net I/σ(I): 6.9 / Num. measured all: 77450 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.63-2.7670.886874512480.7790.3570.9571.989.4
8.73-44.346.60.06120713130.9980.0250.06621.899.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.63 Å44.34 Å
Translation2.63 Å44.34 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.25data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KDB

5kdb


Resolution: 2.644→44.338 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2605 525 5.02 %Random selection
Rwork0.2243 9941 --
obs0.2261 10466 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.87 Å2 / Biso mean: 33.6281 Å2 / Biso min: 1.51 Å2
Refinement stepCycle: final / Resolution: 2.644→44.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 55 85 3161
Biso mean--28.9 19.96 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053154
X-RAY DIFFRACTIONf_angle_d1.2234307
X-RAY DIFFRACTIONf_chiral_restr0.045468
X-RAY DIFFRACTIONf_plane_restr0.006571
X-RAY DIFFRACTIONf_dihedral_angle_d14.0211157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.644-2.910.34121320.29632410254298
2.91-3.3310.29871460.26824602606100
3.331-4.19620.1991050.205625272632100
4.1962-44.34460.24951420.186125442686100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6262-0.2364-0.01640.36620.41770.79060.0280.114-0.01990.2885-0.17220.0246-0.05940.0123-0.10030.7955-0.04080.03560.1637-0.00620.1698-4.2561-5.928433.6553
21.2267-0.2399-0.47770.15230.56992.51940.0886-0.14250.4478-0.0597-0.06620.1033-0.27930.3185-0.18410.67820.0156-0.00190.209-0.02190.3079-0.510410.397823.2043
31.3805-0.41510.12281.08420.41730.4756-0.02430.16450.1746-0.25820.0925-0.2003-0.0560.0691-0.15720.8301-0.03530.03880.2423-0.06640.272310.6416-7.11354.2071
41.3709-1.00650.97562.4831-0.71890.9859-0.082-0.06340.3236-0.0282-0.0311-0.5221-0.1970.13470.13310.45690.00980.07120.2773-0.01520.378420.0984-5.650211.3166
50.88180.4543-1.37041.6596-1.77993.0243-0.0054-0.10480.12960.151-0.0877-0.1682-0.29210.15170.1270.3071-0.01320.00690.2935-0.03250.359414.92477.091220.0795
60.4932-0.29070.17880.57470.30210.8529-0.04330.0528-0.25480.05720.02490.1705-0.16560.1039-0.05930.8780.00060.02160.2237-0.0906-0.09216.2785-7.388113.7323
71.18260.74220.62781.3486-0.48111.2788-0.1496-0.03290.22290.2014-0.0720.2452-0.2631-0.2394-0.32950.1546-0.09440.06410.2891-0.02370.22-9.3472-6.789329.4948
81.54880.2031-0.04612.9004-0.80270.32880.0544-0.22740.0517-0.381-0.21150.25130.5039-0.18060.03330.59740.0165-0.0310.3116-0.02610.162-1.8217-13.742616.6437
90.95420.0064-0.48250.4431-0.60161.07640.0269-0.2189-0.0037-0.4501-0.0082-0.2689-0.0180.21690.28380.73520.03470.01070.2377-0.0250.199315.3627-16.222517.2091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 79 )A17 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 105 )A80 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 142 )A106 - 142
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 170 )A143 - 170
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 219 )A171 - 219
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 301 )A220 - 301
7X-RAY DIFFRACTION7chain 'A' and (resid 302 through 336 )A302 - 336
8X-RAY DIFFRACTION8chain 'A' and (resid 337 through 360 )A337 - 360
9X-RAY DIFFRACTION9chain 'A' and (resid 361 through 409 )A361 - 409

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