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- PDB-4tpn: High-resolution structure of TxtE in the absence of substrate -

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Basic information

Entry
Database: PDB / ID: 4tpn
TitleHigh-resolution structure of TxtE in the absence of substrate
ComponentsPutative P450-like protein
KeywordsOXIDOREDUCTASE / cytochrome / p450 / heme / nitration
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 / : / Putative P450-like protein
Similarity search - Component
Biological speciesStreptomyces scabies (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.18 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: Advisory / Derived calculations ...Advisory / 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 / pdbx_validate_close_contact / pdbx_validate_symm_contact / 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 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.label_alt_id_1 / _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_total / _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)46,30512
Polymers44,8331
Non-polymers1,47211
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.696, 79.436, 112.355
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, 1 molecules A

#1: Protein Putative P450-like protein


Mass: 44832.930 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, 405 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 3.27 Å3/Da / Density % sol: 62.38 %
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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.18→64.862 Å / Num. all: 182976 / Num. obs: 182976 / % possible obs: 94.9 % / Redundancy: 4.9 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.054 / Rsym value: 0.048 / Net I/av σ(I): 6.397 / Net I/σ(I): 13.9 / Num. measured all: 890795
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
1.18-1.244.41.3620.699205225650.7081.3621.181.1
1.24-1.324.90.8640.9120562248330.4270.8641.994
1.32-1.414.90.481.6116838238730.2360.483.396
1.41-1.524.90.2473.2111856225980.1220.2476.297.4
1.52-1.674.90.136103196208630.0640.1310.897.8
1.67-1.8650.0759.996416191190.0370.07517.598.6
1.86-2.1550.04514.584304169090.0220.04527.398.6
2.15-2.6450.03716.372130145430.0180.03735.299.6
2.64-3.734.90.03415.655753112690.0170.03440.498.9
3.73-37.6084.80.03415.53053564040.0170.03442.398.5

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PDB_EXTRACT3.14data extraction
REFMAC5.8.0049refinement
RefinementResolution: 1.18→64.86 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.1734 / WRfactor Rwork: 0.1627 / FOM work R set: 0.8386 / SU B: 1.203 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0319 / SU Rfree: 0.0303 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1711 9227 5 %RANDOM
Rwork0.1625 173667 --
obs0.1629 182894 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.96 Å2 / Biso mean: 21.146 Å2 / Biso min: 10.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.39 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.18→64.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 93 401 3508
Biso mean--20.87 28.88 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193328
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9894587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28222.987154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10915514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0481533
X-RAY DIFFRACTIONr_chiral_restr0.0930.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212597
X-RAY DIFFRACTIONr_mcbond_it1.3981.7411602
X-RAY DIFFRACTIONr_mcangle_it1.3742.6042014
X-RAY DIFFRACTIONr_scbond_it3.0222.1551726
X-RAY DIFFRACTIONr_rigid_bond_restr8.2333328
X-RAY DIFFRACTIONr_sphericity_free7.062596
X-RAY DIFFRACTIONr_sphericity_bonded6.37753540
LS refinement shellResolution: 1.18→1.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 498 -
Rwork0.342 9527 -
all-10025 -
obs--70.73 %

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