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- PDB-4tpo: High-resolution structure of TxtE with bound tryptophan substrate -

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Basic information

Entry
Database: PDB / ID: 4tpo
TitleHigh-resolution structure of TxtE with bound tryptophan substrate
ComponentsPutative P450-like protein
KeywordsOXIDOREDUCTASE / cytochrome / p450 / heme / nitration
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
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 / Resolution: 1.225 Å
AuthorsCahn, J.K.B. / Dodani, S.C. / Brinkmann-Chen, S. / Heinsich, T. / McIntosh, J.A. / Arnold, F.H.
CitationJournal: Chembiochem / Year: 2014
Title: Structural, Functional, and Spectroscopic Characterization of the Substrate Scope of the Novel Nitrating Cytochrome P450 TxtE.
Authors: Dodani, S.C. / Cahn, J.K. / Heinisch, T. / Brinkmann-Chen, S. / McIntosh, J.A. / Arnold, F.H.
History
DepositionJun 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative P450-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,45210
Polymers44,9711
Non-polymers1,4819
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.832, 79.657, 112.554
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, 1 molecules A

#1: Protein Putative P450-like protein


Mass: 44971.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces scabies (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, 418 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.25 M Li2SO4, 0.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2013
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.225→65.021 Å / Num. all: 170299 / Num. obs: 170299 / % possible obs: 98 % / Redundancy: 3.6 % / Rpim(I) all: 0.075 / Rrim(I) all: 0.148 / Rsym value: 0.126 / Net I/av σ(I): 1.859 / Net I/σ(I): 5.6 / Num. measured all: 612659
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
1.225-1.2930.9950.868503226900.6540.995190.1
1.29-1.373.60.6571.286166236980.3980.6571.899.7
1.37-1.463.60.4071.979967222710.2470.4072.799.4
1.46-1.583.70.2373.177670208430.1410.2374.599.7
1.58-1.733.60.166469353191650.0980.1666.199.3
1.73-1.943.80.1324.466118174100.0760.1328.299.7
1.94-2.243.70.1164.656293153150.0670.1169.899
2.24-2.743.80.1134.750298130940.0650.11311.199.6
2.74-3.873.70.1164.337417100830.0680.11611.498.2
3.87-37.6873.60.1194.32087457300.0710.11911.597.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0069refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.14data extraction
RefinementResolution: 1.225→65.02 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.337 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16026 8558 5 %RANDOM
Rwork0.13787 ---
obs0.139 161654 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.38 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.225→65.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 96 409 3609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0193341
X-RAY DIFFRACTIONr_bond_other_d0.0010.023159
X-RAY DIFFRACTIONr_angle_refined_deg2.2561.9854593
X-RAY DIFFRACTIONr_angle_other_deg1.46337241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1730.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213821
X-RAY DIFFRACTIONr_gen_planes_other0.010.02794
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.461.8841622
X-RAY DIFFRACTIONr_mcbond_other3.461.8841621
X-RAY DIFFRACTIONr_mcangle_it4.1032.8222029
X-RAY DIFFRACTIONr_mcangle_other4.1032.8232030
X-RAY DIFFRACTIONr_scbond_it6.3132.3581719
X-RAY DIFFRACTIONr_scbond_other6.162.3171703
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.953.2982530
X-RAY DIFFRACTIONr_long_range_B_refined5.60520.9423258
X-RAY DIFFRACTIONr_long_range_B_other5.43420.1753005
X-RAY DIFFRACTIONr_rigid_bond_restr6.09736499
X-RAY DIFFRACTIONr_sphericity_free27.3965108
X-RAY DIFFRACTIONr_sphericity_bonded13.51356711
LS refinement shellResolution: 1.225→1.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 478 -
Rwork0.326 9813 -
obs--80.73 %

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