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- PDB-2xly: Structural and Mechanistic Analysis of the Magnesium-Independent ... -

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Basic information

Entry
Database: PDB / ID: 2xly
TitleStructural and Mechanistic Analysis of the Magnesium-Independent Aromatic Prenyltransferase CloQ from the Clorobiocin Biosynthetic Pathway
ComponentsCLOQ
KeywordsTRANSFERASE / PT-BARREL / ANTIBIOTIC BIOSYNTHESIS
Function / homology4-hydroxyphenylpyruvate 3-dimethylallyltransferase / Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / prenyltransferase activity / antibiotic biosynthetic process / 4-hydroxyphenylpyruvate 3-dimethylallyltransferase
Function and homology information
Biological speciesSTREPTOMYCES ROSEOCHROMOGENES SUBSP. OSCITANS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMetzger, U. / Keller, S. / Stevenson, C.E.M. / Heide, L. / Lawson, D.M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure and Mechanism of the Magnesium-Independent Aromatic Prenyltransferase Cloq from the Clorobiocin Biosynthetic Pathway.
Authors: Metzger, U. / Keller, S. / Stevenson, C.E.M. / Heide, L. / Lawson, D.M.
History
DepositionJul 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLOQ


Theoretical massNumber of molelcules
Total (without water)35,9541
Polymers35,9541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.570, 135.570, 95.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein CLOQ / AROMATIC PRENYLTRANSFERASE


Mass: 35953.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LIGAND-FREE FORM
Source: (gene. exp.) STREPTOMYCES ROSEOCHROMOGENES SUBSP. OSCITANS (bacteria)
Plasmid: CLOQ-PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q8GHB2
Sequence detailsTHERE IS AN ADDITIONAL TRIPEPTIDE (WITH SEQUENCE GLY-SER- HIS) AT THE N-TERMINUS LEFT OVER AFTER ...THERE IS AN ADDITIONAL TRIPEPTIDE (WITH SEQUENCE GLY-SER- HIS) AT THE N-TERMINUS LEFT OVER AFTER PROTEOLYTIC CLEAVAGE OF THE HIS-TAG

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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: 3.12 Å3/Da / Density % sol: 60.6 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 6.5
Details: VAPOR DIFFUSION. PROTEIN AT 10 MG PER ML WAS MIXED WITH AN EQUAL VOLUME OF 3 M SODIUM FORMATE, 2 MM DITHIOTHREITOL IN 100 MM HEPES BUFFER AT PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.99→23.24 Å / Num. obs: 8365 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.12 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.5
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 12.19 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.73 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0091refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XLQ

2xlq


Resolution: 3.1→23.24 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 18.226 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23586 411 4.9 %RANDOM
Rwork0.17864 ---
obs0.1815 7947 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å2-0 Å20 Å2
2---1.36 Å20 Å2
3---2.72 Å2
Refinement stepCycle: LAST / Resolution: 3.1→23.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 0 2369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212469
X-RAY DIFFRACTIONr_bond_other_d0.0020.021654
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9283368
X-RAY DIFFRACTIONr_angle_other_deg0.9233976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85522.051117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.41715359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7631523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
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_it0.541.51536
X-RAY DIFFRACTIONr_mcbond_other0.0641.5624
X-RAY DIFFRACTIONr_mcangle_it1.07322451
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4463933
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6334.5914
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 38 -
Rwork0.271 573 -
obs--100 %

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