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- PDB-1grr: CHLORAMPHENICOL PHOSPHOTRANSFERASE IN COMPLEX WITH 2-Nac-CHLORAMP... -

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Basic information

Entry
Database: PDB / ID: 1grr
TitleCHLORAMPHENICOL PHOSPHOTRANSFERASE IN COMPLEX WITH 2-Nac-CHLORAMPHENICOL FROM STREPTOMYCES VENEZUELAE
ComponentsCHLORAMPHENICOL 3-O 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 / response to antibiotic / ATP binding
Similarity search - Function
Chloramphenicol phosphotransferase-like / Chloramphenicol phosphotransferase-like protein / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-ACETYL-P-NITROPHENYLSERINOL / Chloramphenicol 3-O phosphotransferase
Similarity search - Component
Biological speciesSTREPTOMYCES VENEZUELAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsIzard, T.
CitationJournal: Protein Sci. / Year: 2001
Title: Structural Basis for Chloramphenicol Tolerance in Streptomyces Venezuelae by Chloramphenicol Phosphotransferase Activity
Authors: Izard, T.
History
DepositionDec 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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

Downloads & links

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Assembly

Deposited unit
A: CHLORAMPHENICOL 3-O PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1853
Polymers18,8341
Non-polymers3502
Water1,45981
1
A: CHLORAMPHENICOL 3-O PHOSPHOTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL 3-O PHOSPHOTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL 3-O PHOSPHOTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL 3-O PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,73912
Polymers75,3374
Non-polymers1,4018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation38_555-y+1/4,-x+1/4,-z+1/41
crystal symmetry operation26_555-x,-y+1/2,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
MethodPQS
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 CHLORAMPHENICOL 3-O PHOSPHOTRANSFERASE / 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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CLC / N-ACETYL-P-NITROPHENYLSERINOL


Mass: 254.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris-HCl1droppH7.5
20.4 Mammonium sulfate1drop
37.5 mg/mlprotein1drop
40.1 MTris-HCl1reservoirpH7.
51.6 Mammonium sulfate1reservoir
64 %acetonitrile1reservoir
72 mMligand1reservoir

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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: 3.1→99 Å / Num. obs: 229617 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 18.41 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 13.9
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.323 / % possible all: 0.9
Reflection
*PLUS
Lowest resolution: 99 Å / Num. obs: 12472 / % possible obs: 98 % / Num. measured all: 229617

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Processing

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

1qhn


Resolution: 2.9→99 Å / Rfactor Rfree error: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 723 5 %RANDOM
Rwork0.278 ---
obs0.278 14463 45 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.9→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 23 81 1424
Refine LS restraints
Refine-IDTypeDev ideal
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_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.463 81 5 %
Rwork0.438 1726 -
obs--71.5 %
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
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 42 Å / Num. reflection obs: 10677 / Rfactor obs: 0.226 / Rfactor Rfree: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.332 / Rfactor obs: 0.336

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