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

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Basic information

Entry
Database: PDB / ID: 2xlq
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 / SAD / 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 21, 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 / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _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

Downloads & links

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Assembly

Deposited unit
A: CLOQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2745
Polymers35,9541
Non-polymers3204
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CLOQ
hetero molecules

A: CLOQ
hetero molecules

A: CLOQ
hetero molecules

A: CLOQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,09520
Polymers143,8144
Non-polymers1,28116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
Buried area10060 Å2
ΔGint-35.6 kcal/mol
Surface area45000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.192, 135.192, 98.132
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: COMPLEX WITH 4-HYDROXYPHENOLPYRUVATE
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details4-HYDROXYPHENYLPYRUVATE: 4-HYDROXYPHENYLPYRUVATE WAS COVALENTLY LINKED THROUGH ITS C2 ATOM TO THE ...4-HYDROXYPHENYLPYRUVATE: 4-HYDROXYPHENYLPYRUVATE WAS COVALENTLY LINKED THROUGH ITS C2 ATOM TO THE SG ATOM OF CYS215 TO GIVE A THIOHEMIKETAL SPECIES REPRESENTED HERE BY 2-HYDROXY-3-(4-HYDROXYPHENYL)PROPANOIC ACID (34H) FORMIC ACID (FMT): SODIUM FORMATE WAS A COMPONENT OF THE PRECIPITANT
Sequence detailsTHERE ARE THREE ADDITIONAL RESIDUES (WITH SEQUENCE GLY-SER- HIS) AT THE N-TERMINUS LEFT OVER AFTER ...THERE ARE THREE ADDITIONAL 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) 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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 9, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.21→31.86 Å / Num. obs: 22556 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 7.75 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.63
Reflection shellResolution: 2.21→2.33 Å / Redundancy: 7.36 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.57 / % possible all: 81.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0091refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.22→95.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.845 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1152 5.1 %RANDOM
Rwork0.165 ---
obs0.167 21394 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2---0.87 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.22→95.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 22 236 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212560
X-RAY DIFFRACTIONr_bond_other_d0.0010.021718
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9423480
X-RAY DIFFRACTIONr_angle_other_deg0.9423.0014129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65722.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43915377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6781522
X-RAY DIFFRACTIONr_chiral_restr0.0910.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
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_it0.7441.51592
X-RAY DIFFRACTIONr_mcbond_other0.1551.5647
X-RAY DIFFRACTIONr_mcangle_it1.44122534
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3783968
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9214.5945
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: 2.22→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 87 -
Rwork0.256 1504 -
obs--96.07 %

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