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- PDB-1qhy: CHLORAMPHENICOL PHOSPHOTRANSFERASE FROM STREPTOMYCES VENEZUELAE I... -

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Basic information

Entry
Database: PDB / ID: 1qhy
TitleCHLORAMPHENICOL PHOSPHOTRANSFERASE FROM STREPTOMYCES VENEZUELAE IN COMPLEX WITH ATPGAMMAS AND CHLORAMPHENICOL
ComponentsCHLORAMPHENICOL 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / CHLORAMPHENICOL / Chloramphenicol 3-O phosphotransferase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionJun 1, 1999Deposition site: BNL / Processing site: NDB
Revision 1.0Jun 7, 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 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1246
Polymers18,8341
Non-polymers1,2905
Water81145
1
A: CHLORAMPHENICOL PHOSPHOTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL PHOSPHOTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL PHOSPHOTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,49724
Polymers75,3374
Non-polymers5,15920
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 area16610 Å2
ΔGint-220 kcal/mol
Surface area26230 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
Components on special symmetry positions
IDModelComponents
11A-1001-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: 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

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Non-polymers , 5 types, 50 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-CLM / CHLORAMPHENICOL / Chloramphenicol


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


Mass: 18.015 Da / Num. of mol.: 45 / 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
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mMprotein1drop
250 mMTris-HCl1drop
30.4 Mammonium sulfate1drop
410 mMmagnesium chloride1drop
510 mMATPgammaS1drop
60.1 MTris-HCl1reservoir
71.14 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: 21331 / % possible obs: 98.1 % / Redundancy: 14.52 % / Rmerge(I) obs: 0.061 / Rsym value: 0.064 / Net I/σ(I): 16.2
Reflection
*PLUS
% possible obs: 99.7 % / Redundancy: 14.26 % / Num. measured all: 304201
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.367

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Processing

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

1qhn


Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 -5 %RANDOM
Rwork0.233 ---
obs0.233 21191 93.6 %-
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 76 45 1441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / Rfactor Rwork: 0.349

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