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- PDB-2xm5: Structural and Mechanistic Analysis of the Magnesium-Independent ... -

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Basic information

Entry
Database: PDB / ID: 2xm5
TitleStructural and Mechanistic Analysis of the Magnesium-Independent Aromatic Prenyltransferase CloQ from the Clorobiocin Biosynthetic Pathway
ComponentsCLOQ
KeywordsTRANSFERASE / PT-BARREL / ANTIBIOTIC BIOSYNTHESIS
Function / homology
Function and homology information


4-hydroxyphenylpyruvate 3-dimethylallyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / prenyltransferase activity / antibiotic biosynthetic process
Similarity search - Function
Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase
Similarity search - Domain/homology
FORMIC ACID / 4-hydroxyphenylpyruvate 3-dimethylallyltransferase
Similarity search - Component
Biological speciesSTREPTOMYCES ROSEOCHROMOGENES SUBSP. OSCITANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 23, 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 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,41411
Polymers35,9381
Non-polymers47610
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.450, 135.450, 99.340
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: 35937.531 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C215S MUTANT SOAKED IN 4-HYDROXYPHENYL PYRUVATE. UNINTERPRETABLE RESIDUAL ELECTRON DENSITY IN ACTIVE SITE PRESUMED TO BE THIS LIGAND.
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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 215 TO SER
Nonpolymer detailsETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS USED AS A CRYOPROTECTANT FORMATE (FMT): SODIUM FORMATE ...ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS USED AS A CRYOPROTECTANT FORMATE (FMT): SODIUM FORMATE WAS A COMPONENT OF THE PRECIPITANT
Sequence detailsTHERE ARE AN ADDITIONAL THREE RESIDUES (WITH SEQUENCE GLY-SER- HIS) AT THE N-TERMINUS LEFT OVER ...THERE ARE AN ADDITIONAL THREE RESIDUES (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 (10 MG/ML) WAS MIXED WITH AN EQUAL VOLUME OF 3 M SODIUM FORMATE, 2 MM DITHIOTHREITOL, 100 MM HEPES PH 6.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→44.09 Å / Num. obs: 39516 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.18 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.12
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 14.47 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.43 / % 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: 1.85→42.83 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.945 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18597 1967 5 %RANDOM
Rwork0.16097 ---
obs0.16224 37537 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-0 Å20 Å2
2---1 Å20 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 31 269 2712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212661
X-RAY DIFFRACTIONr_bond_other_d0.0010.021815
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9353629
X-RAY DIFFRACTIONr_angle_other_deg0.90734374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1115348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84922.348132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98815404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5131527
X-RAY DIFFRACTIONr_chiral_restr0.090.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
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_it0.9151.51641
X-RAY DIFFRACTIONr_mcbond_other0.2491.5667
X-RAY DIFFRACTIONr_mcangle_it1.67622613
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.57231020
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1664.51002
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: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 150 -
Rwork0.252 2706 -
obs--100 %

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