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- PDB-1n97: Crystal Structure of CYP175A1 from Thermus thermophillus strain HB27 -

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Basic information

Entry
Database: PDB / ID: 1n97
TitleCrystal Structure of CYP175A1 from Thermus thermophillus strain HB27
ComponentsCYP175A1
KeywordsELECTRON TRANSPORT / P450
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, E-class, group I / 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 / S,R MESO-TARTARIC ACID / Cytochrome P450
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYano, J.K. / Blasco, F. / Li, H. / Schmid, R.D. / Henne, A. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Preliminary Characterization and Crystal Structure of a Thermostable Cytochrome P450 from Thermus thermophilus
Authors: Yano, J.K. / Blasco, F. / Li, H. / Schmid, R.D. / Henne, A. / Poulos, T.L.
History
DepositionNov 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Aug 16, 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 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _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: CYP175A1
B: CYP175A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,29524
Polymers88,6452
Non-polymers2,65022
Water9,512528
1
A: CYP175A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,52310
Polymers44,3221
Non-polymers1,2019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYP175A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,77214
Polymers44,3221
Non-polymers1,44913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.538, 90.699, 74.516
Angle α, β, γ (deg.)90.00, 99.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYP175A1


Mass: 44322.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cytochrome P450 / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: Q746J6
#2: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.25 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.4 M Na/K Tartrate, 100 mM Na Phosphate/citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.4 Msodium potassium tartrate1reservoir
2100 mMsodium citrate/phosphate1reservoirpH4.2
31 mM1-phenylimidazole1reservoiror 4-phenylimidazole
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1003 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2001
Details: a front end, vertically collimating premirror, double-crystal silicon (111) monochromator with a fixed-height exit beam, toroidal focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1003 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 78342 / Num. obs: 77717 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1000
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 3.1 / % possible all: 89.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 84011 / % possible obs: 94.1 % / Num. measured all: 314845 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 72.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.94

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAG

1fag


Resolution: 1.8→19.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.222 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22229 3639 5.1 %RANDOM
Rwork0.18167 ---
all0.207 78342 --
obs0.18376 67977 91.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.861 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-1.52 Å2
2---0.77 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 178 528 6832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0216438
X-RAY DIFFRACTIONr_bond_other_d0.0030.026170
X-RAY DIFFRACTIONr_angle_refined_deg2.0352.0328733
X-RAY DIFFRACTIONr_angle_other_deg1.004314185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765764
X-RAY DIFFRACTIONr_chiral_restr0.1450.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027046
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021421
X-RAY DIFFRACTIONr_nbd_refined0.2290.21403
X-RAY DIFFRACTIONr_nbd_other0.2560.27100
X-RAY DIFFRACTIONr_nbtor_other0.090.23913
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2378
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.2175
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.237
X-RAY DIFFRACTIONr_mcbond_it1.4361.53849
X-RAY DIFFRACTIONr_mcangle_it2.29226135
X-RAY DIFFRACTIONr_scbond_it3.12232589
X-RAY DIFFRACTIONr_scangle_it4.5154.52598
LS refinement shellResolution: 1.804→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.385 234
Rwork0.314 4082
Refinement TLS params.Method: refined / Origin x: 16.8837 Å / Origin y: 23.7479 Å / Origin z: 17.1449 Å
111213212223313233
T0.0331 Å20.0115 Å20.0008 Å2-0.0278 Å2-0.022 Å2--0.021 Å2
L0.0674 °20.0977 °2-0.0201 °2-0.1451 °2-0.0771 °2--0.0445 °2
S-0.0017 Å °-0.0118 Å °0.0201 Å °-0.015 Å °-0.0015 Å °0.0176 Å °0.0016 Å °-0.0009 Å °0.0032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3851 - 385
2X-RAY DIFFRACTION1BB1 - 3851 - 385
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.028
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.1

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