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- PDB-4egm: The X-ray crystal structure of CYP199A4 in complex with 4-ethylbe... -

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Basic information

Entry
Database: PDB / ID: 4egm
TitleThe X-ray crystal structure of CYP199A4 in complex with 4-ethylbenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Secondary metabolites biosynthesis / transport / catabolism
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-ethylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsZhou, W. / Bell, S.G. / Yang, W. / Zhou, R.M. / Tan, A.B.H. / Wong, L.-L.
CitationJournal: Chemistry / Year: 2012
Title: Investigation of the substrate range of CYP199A4: modification of the partition between hydroxylation and desaturation activities by substrate and protein engineering
Authors: Bell, S.G. / Zhou, R.M. / Yang, W. / Tan, A.B.H. / Gentleman, A.S. / Wong, L.-L. / Zhou, W.
History
DepositionMar 31, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
B: Cytochrome P450
C: Cytochrome P450
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,36735
Polymers178,3504
Non-polymers5,01831
Water4,143230
1
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8669
Polymers44,5871
Non-polymers1,2788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7708
Polymers44,5871
Non-polymers1,1827
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8669
Polymers44,5871
Non-polymers1,2788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8669
Polymers44,5871
Non-polymers1,2788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.864, 143.279, 172.513
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cytochrome P450


Mass: 44587.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2IU02

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Non-polymers , 6 types, 261 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-EGM / 4-ethylbenzoic acid


Mass: 150.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H10O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-tris, 1.45M (NH4)2SO4, 0.1M NaCl, 0.5M Sodium fluoride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 58819 / Num. obs: 58646 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.141 / Rsym value: 0.097 / Net I/σ(I): 15
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 3.58 / Num. unique all: 2886 / Rsym value: 0.567 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNZ

4dnz


Resolution: 2.91→41.57 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.444 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.855 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24919 2970 5.1 %RANDOM
Rwork0.18164 ---
obs0.185 55617 99.27 %-
all-56026 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.352 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0.09 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.91→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12090 0 319 230 12639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212709
X-RAY DIFFRACTIONr_angle_refined_deg1.7192.02817357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74451571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74523.034557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.972151939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.69115116
X-RAY DIFFRACTIONr_chiral_restr0.1060.21874
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0229868
X-RAY DIFFRACTIONr_mcbond_it0.5831.57868
X-RAY DIFFRACTIONr_mcangle_it1.154212674
X-RAY DIFFRACTIONr_scbond_it1.88734841
X-RAY DIFFRACTIONr_scangle_it3.1844.54682
LS refinement shellResolution: 2.906→2.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 220 -
Rwork0.244 3780 -
obs-3780 92.66 %

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