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- PDB-3cla: REFINED CRYSTAL STRUCTURE OF TYPE III CHLORAMPHENICOL ACETYLTRANS... -

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Entry
Database: PDB / ID: 3cla
TitleREFINED CRYSTAL STRUCTURE OF TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE AT 1.75 ANGSTROMS RESOLUTION
ComponentsTYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
KeywordsTRANSFERASE (ACYLTRANSFERASE)
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase / chloramphenicol O-acetyltransferase activity / 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
CHLORAMPHENICOL / : / Chloramphenicol acetyltransferase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.75 Å
AuthorsLeslie, A.G.W.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Refined crystal structure of type III chloramphenicol acetyltransferase at 1.75 A resolution.
Authors: Leslie, A.G.
#1: Journal: To be Published
Title: Crystal Structure of the Asp-199-Asn Mutant of Chloramphenicol Acetyltransferase to 2.35 Angstroms Resolution. Structural Consequences of Disruption of a Buried Salt-Bridge.
Authors: Gibbs, M.R. / Moody, P.C.E. / Leslie, A.G.W.
#2: Journal: Biochemistry / Year: 1990
Title: Evidence for Transition-State Stabilization by Serine-148 in the Catalytic Mechanism of Chloramphenicol Acetyltransferase
Authors: Lewendon, A. / Murray, I.A. / Shaw, W.V. / Gibbs, M.R. / Leslie, A.G.W.
#3: Journal: Biochemistry / Year: 1988
Title: Substitutions in the Active Site of Chloramphenicol Acetyltransferase. Role of a Conserved Aspartate
Authors: Lewendon, A. / Murray, I.A. / Kleanthous, C. / Cullis, P.M. / Shaw, W.V.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Structure of Chloramphenicol Acetyltransferase at 1.75-Angstroms Resolution
Authors: Leslie, A.G.W. / Moody, P.C.E. / Shaw, W.V.
#5: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallization of a Type III Chloramphenicol Acetyl Transferase
Authors: Leslie, A.G.W. / Liddell, J.M. / Shaw, W.V.
History
DepositionJul 9, 1990Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Feb 21, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET 1 ACTUALLY HAS SEVEN STRANDS. RESIDUES 157 - 162 FORM AN EXTENSION TO THE SIX STRANDED ...SHEET SHEET 1 ACTUALLY HAS SEVEN STRANDS. RESIDUES 157 - 162 FORM AN EXTENSION TO THE SIX STRANDED BETA-SHEET OF AN ADJACENT SHEET WHICH SPANS THE SUBUNIT INTERFACE. THE FINAL STRAND, SER 157 - VAL 162, IS IN AN ADJACENT (THREE-FOLD RELATED) SUBUNIT OF THE TRIMER. N OF ASN 159 IS HYDROGEN BONDED TO O OF SER 34. THERE IS A WIDE BETA-BULGE INVOLVING RESIDUES LYS 177, TYR 178, AND LEU 187.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4624
Polymers25,0211
Non-polymers4413
Water3,675204
1
A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules

A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules

A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,38712
Polymers75,0643
Non-polymers1,3239
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 area8880 Å2
ΔGint-77 kcal/mol
Surface area24990 Å2
MethodPISA, PQS
2
A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)152,77524
Polymers150,1296
Non-polymers2,64618
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 area19920 Å2
ΔGint-210 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.600, 107.600, 123.600
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.
2: RESIDUES 157 - 162 FORM AN EXTENSION TO THE SIX STRANDED BETA-SHEET OF AN ADJACENT SHEET WHICH SPANS THE SUBUNIT INTERFACE.
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 TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE


Mass: 25021.494 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-CLM / CHLORAMPHENICOL / Chloramphenicol


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NUMBERING SCHEME ADOPTED IS BASED ON THE ALIGNMENT OF A NUMBER OF CAT SEQUENCES. FOR THE TYPE ...THE NUMBERING SCHEME ADOPTED IS BASED ON THE ALIGNMENT OF A NUMBER OF CAT SEQUENCES. FOR THE TYPE III ENZYME WHOSE COORDINATES ARE PRESENTED IN THIS ENTRY, MET 6 IS THE N-TERMINAL RESIDUE AND THERE IS NO RESIDUE NUMBER 79.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.3 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 %(v/v)MPD1reservoir
210 mMMES1reservior
30.5 mMchloramphenicol1reservoir
40.5 mMcobaltic hexamine chloride1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.75 Å / Rmerge(I) obs: 0.058

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Processing

SoftwareName: DERIV / Classification: refinement
RefinementResolution: 1.75→6 Å / Rfactor Rwork: 0.157
Refinement stepCycle: LAST / Resolution: 1.75→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 22 204 1932
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 6 Å / Num. reflection obs: 27300 / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 3.6 Å2
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 3

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