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- PDB-6laa: Crystal structure of full-length CYP116B46 from Tepidiphilus ther... -

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Basic information

Entry
Database: PDB / ID: 6laa
TitleCrystal structure of full-length CYP116B46 from Tepidiphilus thermophilus
ComponentsCytochrome P450
KeywordsHYDROLASE / ANTIBIOTICS / BIOSYNTHESIS
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding / nucleotide binding / heme binding
Similarity search - Function
: / Dimethylamine monooxygenase subunit DmmA-like, N-terminal domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase NAD-binding domain ...: / Dimethylamine monooxygenase subunit DmmA-like, N-terminal domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase NAD-binding domain / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
CARBONATE ION / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Cytochrome P450
Similarity search - Component
Biological speciesTepidiphilus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsZhang, L.L. / Ko, T.P. / Huang, J.W. / Liu, W.D. / Chen, C.C. / Guo, R.T.
CitationJournal: Nat Commun / Year: 2020
Title: Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase.
Authors: Zhang, L.L. / Xie, Z.Z. / Liu, Z.W. / Zhou, S.Y. / Ma, L.X. / Liu, W.D. / Huang, J.W. / Ko, T.P. / Li, X.Q. / Hu, Y.C. / Min, J. / Yu, X.J. / Guo, R.T. / Chen, C.C.
History
DepositionNov 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.pdbx_descriptor / _struct.title / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,85421
Polymers89,5451
Non-polymers2,30920
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-23 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.715, 94.715, 242.641
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 / CYP116B46


Mass: 89544.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tepidiphilus thermophilus (bacteria) / Plasmid: pRSF-Duet I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K6ITW2

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Non-polymers , 7 types, 561 molecules

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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CO3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.04 Å3/Da / Density % sol: 59.52 % / Mosaicity: 0.487 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: Na/K phosphate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 10, 2019
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.13→25 Å / Num. obs: 62367 / % possible obs: 99.7 % / Redundancy: 16.5 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.028 / Rrim(I) all: 0.113 / Χ2: 0.89 / Net I/σ(I): 6 / Num. measured all: 1025951
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.13-2.2115.21.50261510.8230.3871.5530.514100
2.21-2.2916.41.0461220.9120.261.0720.527100
2.29-2.416.70.74961410.9490.1860.7720.543100
2.4-2.5316.80.51561830.9730.1280.5310.559100
2.53-2.68170.34561870.9850.0850.3560.604100
2.68-2.8917.20.22562110.9930.0550.2310.675100
2.89-3.1817.40.13862240.9970.0340.1430.82899.9
3.18-3.6417.30.08562830.9980.0210.0871.185100
3.64-4.5815.60.05862610.9990.0150.061.66398.8
4.58-25150.04666040.9990.0120.0481.84398.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GII

6gii


Resolution: 2.13→24.11 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2101 3114 5 %
Rwork0.1676 59162 -
obs0.1698 62276 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.17 Å2 / Biso mean: 46.2346 Å2 / Biso min: 23.4 Å2
Refinement stepCycle: final / Resolution: 2.13→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 147 541 6796
Biso mean--42.19 51.75 -
Num. residues----753
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.13-2.210.2953050.23455789609499
2.21-2.30.27723050.216757976102100
2.3-2.40.27373070.205758456152100
2.4-2.530.24483100.192158836193100
2.53-2.680.2183090.180558796188100
2.69-2.890.26233110.188859036214100
2.89-3.180.2283110.186859066217100
3.18-3.640.2433140.171759656279100
3.64-4.580.17663130.13735944625799
4.58-24.110.16353290.15096251658099

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