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- PDB-1tuw: Structural and Functional Analysis of Tetracenomycin F2 Cyclase f... -

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Basic information

Entry
Database: PDB / ID: 1tuw
TitleStructural and Functional Analysis of Tetracenomycin F2 Cyclase from Streptomyces glaucescens: A Type-II Polyketide Cyclase
ComponentsTetracenomycin polyketide synthesis protein tcmI
KeywordsUNKNOWN FUNCTION / dimeric ??? ferredoxin-like fold tetracenomycin C biosynthesis
Function / homology
Function and homology information


tetracenomycin F2 cyclase / polyketide biosynthetic process / antibiotic biosynthetic process / lyase activity
Similarity search - Function
Dimeric alpha+beta barrel. / Polyketide synthesis cyclase / Polyketide synthesis cyclase superfamily / Polyketide synthesis cyclase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tetracenomycin F2 cyclase
Similarity search - Component
Biological speciesStreptomyces glaucescens (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.9 Å
AuthorsThompson, T.B. / Katayama, K. / Watanabe, K. / Hutchinson, C.R. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural and functional analysis of tetracenomycin F2 cyclase from Streptomyces glaucescens. A type II polyketide cyclase.
Authors: Thompson, T.B. / Katayama, K. / Watanabe, K. / Hutchinson, C.R. / Rayment, I.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Tetracenomycin polyketide synthesis protein tcmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9742
Polymers12,8771
Non-polymers961
Water1,42379
1
A: Tetracenomycin polyketide synthesis protein tcmI
hetero molecules

A: Tetracenomycin polyketide synthesis protein tcmI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9474
Polymers25,7552
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area4420 Å2
ΔGint-68 kcal/mol
Surface area10670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.7, 46.7, 188.3
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Tetracenomycin polyketide synthesis protein tcmI


Mass: 12877.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces glaucescens (bacteria) / Gene: TCMI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39890
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 278 K / Method: microbatch / pH: 7.5
Details: Crystals of tetracenomycin F2 cyclase were grown by microbatch from a solution composed of 2.2 M (NH4)2SO4, 3 mg/ml protein, 50 mM HEPES pH 7.5 at 4 C (11). Large crystals were obtained by ...Details: Crystals of tetracenomycin F2 cyclase were grown by microbatch from a solution composed of 2.2 M (NH4)2SO4, 3 mg/ml protein, 50 mM HEPES pH 7.5 at 4 C (11). Large crystals were obtained by macroseeding with small crystals (0.06 mm x 0.08 mm) washed in macroseeding 1.4 M (NH4)2SO4, 50 mM HEPES pH 7.5 to slightly dissolve the crystal surfaces. After 3 to 4 weeks the crystals attained a size of 0.3 x 0.3 x 0.6 mm. Crystals of the selenomethionine labeled protein were obtained in a similar manner., Micro batch, temperature 278K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Mar 1, 2000 / Details: gobel
RadiationMonochromator: Gobel mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 11605 / Num. obs: 11355 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 23.1
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 5.4 / % possible all: 84

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Processing

Software
NameClassification
Histardata collection
XDSdata reduction
SOLVEphasing
TNTrefinement
HISTARdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.245 480 random
Rwork0.199 --
all0.199 9599 -
obs0.199 9599 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 5 79 934
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.61
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_dihedral_angle_d19.3

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