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- PDB-1qhs: CHLORAMPHENICOL PHOSPHOTRANSFERASE IN COMPLEX WITH CHLORAMPHENICO... -

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Basic information

Entry
Database: PDB / ID: 1qhs
TitleCHLORAMPHENICOL PHOSPHOTRANSFERASE IN COMPLEX WITH CHLORAMPHENICOL FROM STREPTOMYCES VENEZUELAE
ComponentsPROTEIN (CHLORAMPHENICOL PHOSPHOTRANSFERASE)
KeywordsTRANSFERASE / KINASE / ANTIBIOTIC RESISTANCE / PHOSPHORYLATION / MONONUCLEOTIDE BINDING FOLD
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / kinase activity / phosphorylation / response to antibiotic / ATP binding
Similarity search - Function
Chloramphenicol phosphotransferase-like / Chloramphenicol phosphotransferase-like protein / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CHLORAMPHENICOL / Chloramphenicol 3-O phosphotransferase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsIzard, T.
CitationJournal: Embo J. / Year: 2000
Title: The Crystal Structures of Chloramphenicol Phosphotransferase Reveal a Novel Inactivation Mechanism
Authors: Izard, T. / Ellis, J.
History
DepositionMay 28, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CHLORAMPHENICOL PHOSPHOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6735
Polymers18,8341
Non-polymers8384
Water1,36976
1
A: PROTEIN (CHLORAMPHENICOL PHOSPHOTRANSFERASE)
hetero molecules

A: PROTEIN (CHLORAMPHENICOL PHOSPHOTRANSFERASE)
hetero molecules

A: PROTEIN (CHLORAMPHENICOL PHOSPHOTRANSFERASE)
hetero molecules

A: PROTEIN (CHLORAMPHENICOL PHOSPHOTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,69120
Polymers75,3374
Non-polymers3,35416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
crystal symmetry operation26_555-x,-y+1/2,z1
crystal symmetry operation38_555-y+1/4,-x+1/4,-z+1/41
Buried area12830 Å2
ΔGint-250 kcal/mol
Surface area27970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)200.000, 200.000, 200.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein PROTEIN (CHLORAMPHENICOL PHOSPHOTRANSFERASE) / CPT


Mass: 18834.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces venezuelae (bacteria) / Strain: ISP5230
References: UniProt: Q56148, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CLM / CHLORAMPHENICOL / Chloramphenicol


Mass: 323.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 8.8 Å3/Da / Density % sol: 86 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
250 mMTris-HCl1drop
30.4 Mammonium sulfate1drop
44 %acetonitrile1drop
52 mMCm1drop
610 mMmagnesium chloride1drop
70.1 MTris-HCl1reservoir
81.14 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 20175 / % possible obs: 93 % / Redundancy: 27.24 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QHN

1qhn


Resolution: 2.8→99 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 5357414.67 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 827 4.8 %RANDOM
Rwork0.226 ---
obs0.226 17118 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.9827 Å2 / ksol: 0.353166 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 50 76 1446
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.691.5
X-RAY DIFFRACTIONc_mcangle_it5.722
X-RAY DIFFRACTIONc_scbond_it7.252
X-RAY DIFFRACTIONc_scangle_it10.122.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 133 4.8 %
Rwork0.315 2652 -
obs--100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CLM.PAR
X-RAY DIFFRACTION4ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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