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- PDB-1qca: QUADRUPLE MUTANT Q92C, N146F, Y168F, I172V TYPE III CAT COMPLEXED... -

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Basic information

Entry
Database: PDB / ID: 1qca
TitleQUADRUPLE MUTANT Q92C, N146F, Y168F, I172V TYPE III CAT COMPLEXED WITH FUSIDIC ACID. CRYSTALS GROWN AT PH 6.3. X-RAY DATA COLLECTED AT ROOM TEMPERATURE
ComponentsTYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
KeywordsTRANSFERASE (ACYLTRANSFERASE) / CHLORAMPHENICOL / FUSIDATE / STEROID
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
: / FUSIDIC ACID / Chloramphenicol acetyltransferase 3
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsLeslie, A.G.W.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Steroid recognition by chloramphenicol acetyltransferase: engineering and structural analysis of a high affinity fusidic acid binding site.
Authors: Murray, I.A. / Cann, P.A. / Day, P.J. / Derrick, J.P. / Sutcliffe, M.J. / Shaw, W.V. / Leslie, A.G.
#1: Journal: Annu.Rev.Biophys.Biophys.Chem. / Year: 1991
Title: Chloramphenicol Acetyltransferase
Authors: Shaw, W.V. / Leslie, A.G.W.
#2: 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.
#3: 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.
History
DepositionAug 3, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6344
Polymers25,0001
Non-polymers6353
Water2,594144
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)76,90212
Polymers74,9993
Non-polymers1,9049
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 area9800 Å2
ΔGint-48 kcal/mol
Surface area24990 Å2
MethodPISA, PQS
2
A: TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)153,80524
Polymers149,9976
Non-polymers3,80718
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 area21330 Å2
ΔGint-142 kcal/mol
Surface area48620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.810, 107.810, 124.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-222-

CO

21A-223-

CO

31A-302-

HOH

41A-303-

HOH

51A-328-

HOH

61A-333-

HOH

DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: MET 6 .. LYS 219 120 DEGREE ROTATION ABOUT Z SYMMETRY1 1 -0.499953 -0.866025 0.000000 0.00000 SYMMETRY2 1 0.866026 -0.500047 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: MET 6 .. LYS 219 120 DEGREE ROTATION ABOUT Z SYMMETRY1 2 -0.500047 0.866025 0.000000 0.00000 SYMMETRY2 2 -0.866026 -0.499953 0.000000 0.00000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein TYPE III CHLORAMPHENICOL ACETYLTRANSFERASE / CAT III


Mass: 24999.553 Da / Num. of mol.: 1 / Mutation: Q92C, N146F, Y168F, I172V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria)
Description: TRANSMISSIBLE PLASMID R387 ISOLATED FROM SHIGELLA FLEXNERI
Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101
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-FUA / FUSIDIC ACID


Mass: 516.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H48O6 / Comment: antibiotic, Antimicrobial*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE ARE TWO COBALT IONS (BOTH OF WHICH LIE ON CRYSTALLOGRAPHIC TWO-FOLD AXES) WHICH PLAY A ...THERE ARE TWO COBALT IONS (BOTH OF WHICH LIE ON CRYSTALLOGRAPHIC TWO-FOLD AXES) WHICH PLAY A CRUCIAL ROLE IN STABILIZING THE CRYSTAL LATTICE (LESLIE, 1990). CO 222 IS TETRAHEDRALLY COORDINATED BY OE2 GLU 23 AND ND1 HIS 27 FROM TWO SYMMETRY-RELATED MOLECULES. CO 223 IS BELIEVED TO BE A COBALT HEXAMMINE GROUP.
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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growpH: 6.3 / Details: pH 6.3
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.7 mg/mlprotein11
210 mMMES11or supplemented with 0.5 mM sodium fusidate
310 mMMES12
42-4 %(v/v)MPD12
51 mMhexamine cobalt(III) chloride12
61 mMchloramphenicol12can be replaced by 0.5mM sodium fusidate
70.1 mMdithiothreitol12

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418 Å
DetectorDetector: IMAGE PLATE / Date: Aug 27, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15.6 Å / Num. obs: 14238 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.095
Reflection
*PLUS
Num. measured all: 68511

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Processing

Software
NameClassification
PROLSQrefinement
MOSFLMdata reduction
RefinementResolution: 2.2→6 Å / 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 A STARTING MODEL. CRYST1 TEXT TO EXPLAIN UNUSUAL UNIT-CELL ...Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT USING THE REFINED 1.75 ANGSTROMS RESOLUTION STRUCTURE OF THE WILD-TYPE ENZYME AS A STARTING MODEL. CRYST1 TEXT TO EXPLAIN UNUSUAL UNIT-CELL DATA: HEXAGONAL SETTING FOR R32 HOH 328 LIES ON A CRYSTALLOGRAPHIC TWO-FOLD AXIS AND IS NOT A TRUE SOLVENT MOLECULE, BUT IS IN MODELLING DENSITY SURROUNDING THE COBALT ION CO223 (ALSO ON THE TWO-FOLD AXIS). PRESUMABLY THIS DENSITY IS DUE TO THE HEXAMMINE GROUP (THE CRYSTALS WERE GROWN IN THE PRESENCE OF COBALT HEXAMMINE).
RfactorNum. reflection% reflection
obs0.174 13517 99 %
Displacement parametersBiso mean: 19.9 Å2
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 39 144 1869
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0490.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0590.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.343
X-RAY DIFFRACTIONp_mcangle_it4.515
X-RAY DIFFRACTIONp_scbond_it6.165
X-RAY DIFFRACTIONp_scangle_it7.727
X-RAY DIFFRACTIONp_plane_restr0.015
X-RAY DIFFRACTIONp_chiral_restr0.1660.15
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.240.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2150.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor14.815
X-RAY DIFFRACTIONp_orthonormal_tor2820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROTIN/PROLSQ / Classification: refinement
Refine LS restraints
*PLUS
Type: p_plane_restr / Dev ideal target: 0.02

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