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- PDB-5d40: Crystal structure of the 5-selective H176Y mutant of Cytochrome TxtE -

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Basic information

Entry
Database: PDB / ID: 5d40
TitleCrystal structure of the 5-selective H176Y mutant of Cytochrome TxtE
ComponentsP450-like protein
KeywordsOXIDOREDUCTASE / cytochrome / p450 / heme / regioselectivity / F/G loop
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
4-nitrotryptophan synthase / 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 / TRYPTOPHAN / Putative P450-like protein
Similarity search - Component
Biological speciesStreptomyces scabies (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å
AuthorsCahn, J.K.B. / Dodani, S.C. / Arnold, F.H.
Funding support United States, 2items
OrganizationGrant numberCountry
Gordon and Betty MooreGBMF2809 United States
US Army Research OfficeW911NF-09-0001 United States
CitationJournal: Nat.Chem. / Year: 2016
Title: Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models.
Authors: Dodani, S.C. / Kiss, G. / Cahn, J.K. / Su, Y. / Pande, V.S. / Arnold, F.H.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P450-like protein
B: P450-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,82716
Polymers94,3212
Non-polymers2,50614
Water20,8071155
1
A: P450-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1655
Polymers47,1601
Non-polymers1,0054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P450-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,66111
Polymers47,1601
Non-polymers1,50110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.721, 99.207, 105.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein P450-like protein


Mass: 47160.496 Da / Num. of mol.: 2 / Mutation: H176Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabies (strain 87.22) (bacteria)
Strain: 87.22 / Gene: SCAB_31831 / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: C9ZDC6

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Non-polymers , 5 types, 1169 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1155 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 200mM MgCl2, 100mM Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2015
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.15→72.206 Å / Num. all: 120407 / Num. obs: 120407 / % possible obs: 97.5 % / Redundancy: 4.7 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.113 / Rsym value: 0.1 / Net I/av σ(I): 5.349 / Net I/σ(I): 8 / Num. measured all: 564788
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.51-1.5940.6011.160558152510.3380.6012.285.4
1.59-1.694.80.4291.781582168260.2180.4293.299.8
1.69-1.84.60.3182.372936157640.1650.3184.199.1
1.8-1.954.90.2083.472893148330.1060.2085.999.8
1.95-2.134.70.1374.763498135960.0710.1377.999.4
2.13-2.384.90.16.460901123930.0510.110.599.8
2.38-2.754.70.0787.951962109720.040.07812.399.6
2.75-3.3750.0598.94658793170.030.05915.799.8
3.37-4.774.70.0499.93445373000.0250.0491999.6
4.77-38.4694.70.044101941841550.0220.04417.799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.99 Å38.47 Å
Translation5.99 Å38.47 Å

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHASER2.5.6phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TPN

4tpn


Resolution: 1.51→72.206 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.2062 / WRfactor Rwork: 0.1384 / FOM work R set: 0.765 / SU B: 3.777 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0952 / SU Rfree: 0.0864 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 6063 5 %RANDOM
Rwork0.1492 ---
obs0.1525 114245 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.42 Å2 / Biso mean: 13.754 Å2 / Biso min: 3.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.76 Å2
Refinement stepCycle: final / Resolution: 1.51→72.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 171 1155 7610
Biso mean--12.2 30.89 -
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196696
X-RAY DIFFRACTIONr_bond_other_d0.0010.026371
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.9819180
X-RAY DIFFRACTIONr_angle_other_deg0.931314592
X-RAY DIFFRACTIONr_chiral_restr0.1450.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217653
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021599
X-RAY DIFFRACTIONr_mcbond_it1.7941.0073254
X-RAY DIFFRACTIONr_mcbond_other1.7941.0073253
X-RAY DIFFRACTIONr_mcangle_it2.1331.5174067
X-RAY DIFFRACTIONr_rigid_bond_restr3.929313067
X-RAY DIFFRACTIONr_sphericity_free34.0515386
X-RAY DIFFRACTIONr_sphericity_bonded9.656513657
LS refinement shellResolution: 1.508→1.547 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 288 -
Rwork0.262 6265 -
all-6553 -
obs--72.68 %

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