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- PDB-1zdy: Co-crystal structure of Orf2 an aromatic prenyl transferase from ... -

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Basic information

Entry
Database: PDB / ID: 1zdy
TitleCo-crystal structure of Orf2 an aromatic prenyl transferase from Streptomyces sp. strain CL190 complexed with TAPS
ComponentsAromatic prenyltransferase
KeywordsTRANSFERASE / novel aromatic prenyltransferase barrel fold / PT-barrel
Function / homologyAromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metal ion binding / Chem-T3A / Prenyltransferase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsKuzuyama, T. / Noel, J.P. / Richard, S.B.
CitationJournal: Nature / Year: 2005
Title: Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products.
Authors: Kuzuyama, T. / Noel, J.P. / Richard, S.B.
History
DepositionApr 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 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
Remark 999SEQUENCE AT THE TIME OF PROCESSING THERE WAS NO DATABASE MATCH FOR THIS SEQUENCE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0212
Polymers33,7781
Non-polymers2431
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.145, 91.451, 48.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer

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Components

#1: Protein Aromatic prenyltransferase


Mass: 33778.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: CL190 / Plasmid: PHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4R2T2
#2: Chemical ChemComp-T3A / N-(TRIS(HYDROXYMETHYL)METHYL)-3-AMINOPROPANESULFONIC ACID


Mass: 243.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO6S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.4 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 279 K / Method: evaporation / pH: 8.5
Details: 28% PEG 4000, 0.3M Magnesium Nitrate, 2mM DTT, 0.1M PIPES, pH 8.5, EVAPORATION, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 16, 2004 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 63586 / Num. obs: 46752 / % possible obs: 78.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.84 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.097 / Net I/σ(I): 37.34
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 1.94 % / Mean I/σ(I) obs: 38.9 / Rsym value: 0.515 / % possible all: 50.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→30.23 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1311741.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2333 5 %RANDOM
Rwork0.222 ---
all0.222 ---
obs0.222 46752 80.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.261 Å2 / ksol: 0.344642 e/Å3
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---2.21 Å20 Å2
3---1.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.44→30.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 15 404 2750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 147 5.8 %
Rwork0.303 2394 -
obs--24.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5taps.param

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