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- PDB-2xm7: Structural and Mechanistic Analysis of the Magnesium-Independent ... -

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Basic information

Entry
Database: PDB / ID: 2xm7
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
(2R)-2-HYDROXY-3-(4-HYDROXYPHENYL)PROPANOIC ACID / FORMIC ACID / 4-hydroxyphenylpyruvate 3-dimethylallyltransferase
Similarity search - Component
Biological speciesSTREPTOMYCES ROSEOCHROMOGENES SUBSP. OSCITANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 25, 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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

Downloads & links

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Assembly

Deposited unit
A: CLOQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,45010
Polymers35,8831
Non-polymers5669
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.340, 135.340, 98.640
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: 35883.480 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: R66S MUTANT COMPLEXED WITH 4-HYDROXYPHENYL PYRUVATE
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-34H / (2R)-2-HYDROXY-3-(4-HYDROXYPHENYL)PROPANOIC ACID


Mass: 182.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 66 TO SER
Has protein modificationY
Nonpolymer detailsETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS USED AS A CRYOPROTECTANT (2R)-2-HYDROXY-3-(4- ...ETHYLENE GLYCOL (EDO): ETHYLENE GLYCOL WAS USED AS A CRYOPROTECTANT (2R)-2-HYDROXY-3-(4-HYDROXYPHENYL)PROPANOIC ACID (34H): 4-HYDROXYPHENYLPYRUVATE WAS COVALENTLY LINKED THROUGH ITS C2 ATOM TO THE SG ATOM OF CYS215 TO GIVE A THIOHEMIKETAL SPECIES FORMIC ACID (FMT): SODIUM FORMATE WAS A COMPONENT OF THE PRECIPITANT
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 (10 MG/ML) 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: 0.951
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.951 Å / Relative weight: 1
ReflectionResolution: 2.22→51.57 Å / Num. obs: 23029 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.45 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.83
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 6.91 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.22 / % 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: 2.22→43.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.237 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20959 1169 5.1 %RANDOM
Rwork0.17386 ---
obs0.17572 21654 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.787 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.22→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 38 155 2564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212548
X-RAY DIFFRACTIONr_bond_other_d0.0030.021732
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9423461
X-RAY DIFFRACTIONr_angle_other_deg0.9423.0014148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26321.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73815378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4881526
X-RAY DIFFRACTIONr_chiral_restr0.0860.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212912
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02584
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_it0.881.51580
X-RAY DIFFRACTIONr_mcbond_other0.1961.5643
X-RAY DIFFRACTIONr_mcangle_it1.69822505
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5663968
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1824.5950
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: 2.216→2.273 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 95 -
Rwork0.255 1547 -
obs--98.5 %

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