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- PDB-1cia: REPLACEMENT OF CATALYTIC HISTIDINE-195 OF CHLORAMPHENICOL ACETYLT... -

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Basic information

Entry
Database: PDB / ID: 1cia
TitleREPLACEMENT OF CATALYTIC HISTIDINE-195 OF CHLORAMPHENICOL ACETYLTRANSFERASE: EVIDENCE FOR A GENERAL BASE ROLE FOR GLUTAMATE
ComponentsCHLORAMPHENICOL ACETYLTRANSFERASE
KeywordsTRANSFERASE(ACYLTRANSFERASE)
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase activity / chloramphenicol O-acetyltransferase / response to antibiotic
Similarity search - Function
Chloramphenicol acetyltransferase, active site / Chloramphenicol acetyltransferase active site. / Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / Chloramphenicol acetyltransferase / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / Chloramphenicol acetyltransferase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLeslie, A.G.W. / Gibbs, M.R.
Citation
Journal: Biochemistry / Year: 1994
Title: Replacement of catalytic histidine-195 of chloramphenicol acetyltransferase: evidence for a general base role for glutamate.
Authors: Lewendon, A. / Murray, I.A. / Shaw, W.V. / Gibbs, M.R. / Leslie, A.G.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Refined Crystal Structure of Type III Chloramphenicol Acetyltransferase at 1.75 Angstroms Resolution
Authors: Leslie, A.G.W.
History
DepositionJul 19, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET RESIDUES 157 - 162 FORM AN EXTENSION TO THE SIX-STRANDED BETA SHEET OF AN ADJACENT SUBUNIT OF ...SHEET RESIDUES 157 - 162 FORM AN EXTENSION TO THE SIX-STRANDED BETA SHEET OF AN ADJACENT SUBUNIT OF THE TRIMER, RESULTING IN A SEVEN-STRANDED SHEET THAT SPANS THE SUBUNIT INTERFACE. THERE IS A WIDE BETA-BULGE INVOLVING RESIDUES LYS 177, TYR 178 AND LEU 187

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2074
Polymers25,0111
Non-polymers1963
Water2,234124
1
A: CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,62212
Polymers75,0343
Non-polymers5889
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7440 Å2
ΔGint-45 kcal/mol
Surface area25160 Å2
MethodPISA, PQS
2
A: CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)151,24524
Polymers150,0696
Non-polymers1,17618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area16690 Å2
ΔGint-147 kcal/mol
Surface area48880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.640, 107.640, 124.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Atom site foot note1: THERE IS A WIDE BETA-BULGE INVOLVING RESIDUES LYS 177, TYR 178 AND LEU 187.
Components on special symmetry positions
IDModelComponents
11A-222-

CO

21A-223-

CO

31A-310-

HOH

41A-311-

HOH

51A-341-

HOH

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Components

#1: Protein CHLORAMPHENICOL ACETYLTRANSFERASE


Mass: 25011.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P00484, chloramphenicol O-acetyltransferase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CATALYTICALLY ESSENTIAL HIS 195 (WHICH ACTS AS A GENERAL BASE IN THE PROPOSED CATALYTIC ...THE CATALYTICALLY ESSENTIAL HIS 195 (WHICH ACTS AS A GENERAL BASE IN THE PROPOSED CATALYTIC MECHANISM) HAS BEEN MUTATED TO GLUTAMINE. THE RESULTANT ENZYME SHOWS AN ACTIVITY FIVE ORDERS OF MAGNITUDE LOWER THAN WILD TYPE, ALTHOUGH THE KM VALUES FOR BOTH CHLORAMPHENICOL AND ACETYL COA ARE ALMOST UNCHANGED. THE RESIDUAL ACTIVITY DETECTED IS ALMOST CERTAINLY DUE TO MISINCORPORATION OF HISTIDINE AT RESIDUE 195.
Nonpolymer detailsTHE COBALT IONS PLAY A CRUCIAL ROLE IN STABILIZING THE CRYSTAL LATTICE (LESLIE, 1990). IN SPITE OF ...THE COBALT IONS PLAY A CRUCIAL ROLE IN STABILIZING THE CRYSTAL LATTICE (LESLIE, 1990). IN SPITE OF THE FACT THAT CHLORAMPHENICOL WAS PRESENT IN THE CRYSTALLIZATION MOTHER LIQUOR, THERE IS NO EVIDENCE FOR BOUND CHLORAMPHENICOL IN THE STRUCTURE. INSTEAD, A MOLECULE OF 2-MERCAPTOETHANOL (WHICH WAS PRESENT AT 5MM CONCENTRATION) IS FOUND IN THE CHLORAMPHENICOL BINDING POCKET.
Sequence detailsTHE AMINO ACID NUMBERING SCHEME ADOPTED IS BASED ON THE ALIGNMENT OF SEVERAL CAT SEQUENCES. FOR THE ...THE AMINO ACID NUMBERING SCHEME ADOPTED IS BASED ON THE ALIGNMENT OF SEVERAL CAT SEQUENCES. FOR THE TYPE III ENZYME WHOSE COORDINATES ARE GIVEN HERE, MET 6 IS THE N-TERMINAL RESIDUE AND THERE IS NO RESIDUE 79.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.3 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
210 mMMES11
32-4 %MPD12
410 mMMES12
51 mMchloramphenicol12
60.5 mMhexaamminecobalt(III)chloride12
75 mM2-mercaptoethanol12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 9485 / % possible obs: 97 % / Num. measured all: 23710 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
Rmerge(I) obs: 0.103

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.5→6 Å / Rfactor obs: 0.131 / σ(F): 0
Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING THE REFINED 1.75 ANGSTROMS RESOLUTION STRUCTURE OF THE WILD TYPE ENZYME AS AN INITIAL MODEL.
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 6 124 1815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 0 / Rfactor all: 0.131
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.044
X-RAY DIFFRACTIONp_planar_d0.050.062
X-RAY DIFFRACTIONp_plane_restr0.020.019
X-RAY DIFFRACTIONp_chiral_restr0.150.19

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