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- PDB-6x7q: Chloramphenicol acetyltransferase type III in complex with chlora... -

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Basic information

Entry
Database: PDB / ID: 6x7q
TitleChloramphenicol acetyltransferase type III in complex with chloramphenicol and acetyl-oxa(dethia)-CoA
ComponentsChloramphenicol acetyltransferase 3
KeywordsTRANSFERASE / Chloramphenicol acetyltransferase / Antibiotic resistance
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-like domain superfamily
Similarity search - Domain/homology
CHLORAMPHENICOL / DI(HYDROXYETHYL)ETHER / acetyl-oxa(dethia)-CoA / Chloramphenicol acetyltransferase 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsBenjamin, A.B. / Stunkard, L.M. / Ling, J. / Nice, J.N. / Lohman, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM140290 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Structures of chloramphenicol acetyltransferase III and Escherichia coli beta-keto-acylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(de-thia)CoA
Authors: Benjamin, A.B. / Stunkard, L.M. / Ling, J. / Nice, J.N. / Lohman, J.R.
History
DepositionMay 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 2.0Jul 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_poly / entity_poly_seq / pdbx_audit_support / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_contact_author.id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine.pdbx_overall_ESU_R / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _software.classification / _software.name / _software.version / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Description: Sequence discrepancy
Details: N-terminal residues from cloning artifacts were improperly modeled
Provider: author / Type: Coordinate replacement
Revision 2.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloramphenicol acetyltransferase 3
B: Chloramphenicol acetyltransferase 3
C: Chloramphenicol acetyltransferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,05613
Polymers75,2743
Non-polymers3,78110
Water14,520806
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-69 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.918, 106.918, 126.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-303-

ZN

21A-624-

HOH

31B-666-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Chloramphenicol acetyltransferase 3 / Chloramphenicol acetyltransferase III / CAT-III


Mass: 25091.480 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cat3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00484, chloramphenicol O-acetyltransferase

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Non-polymers , 6 types, 816 molecules

#2: Chemical ChemComp-UTA / acetyl-oxa(dethia)-CoA / (3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl acetate


Mass: 793.505 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O18P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM magnesium chloride, 100 mM sodium citrate:citric acid, pH 5.5, 46% PEG400
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2019
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 84122 / % possible obs: 100 % / Redundancy: 14.5 % / Biso Wilson estimate: 20.371 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.04 / Rrim(I) all: 0.152 / Rsym value: 0.092 / Χ2: 1.047 / Net I/av σ(I): 19.583 / Net I/σ(I): 23.5
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.261 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8292 / CC1/2: 0.813 / CC star: 0.947 / Rpim(I) all: 0.343 / Rrim(I) all: 1.308 / Rsym value: 1.231 / Χ2: 1.001 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
ARP/wARPmodel building
Cootmodel building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CLA

3cla


Resolution: 1.68→34.33 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.1508 / FOM work R set: 0.8509 / SU B: 2.217 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0945 / SU Rfree: 0.0981 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 4005 4.8 %RANDOM
Rwork0.1592 ---
obs0.1612 80050 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.15 Å2 / Biso mean: 18.716 Å2 / Biso min: 8.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.68→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5276 0 236 809 6321
Biso mean--34.21 32.51 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125900
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165161
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.6728074
X-RAY DIFFRACTIONr_angle_other_deg0.5771.58212075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.9299.530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35910961
X-RAY DIFFRACTIONr_chiral_restr0.090.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026679
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021257
LS refinement shellResolution: 1.68→1.722 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.267 278 -
Rwork0.266 5743 -
obs--98.33 %

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