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- PDB-4xxr: Atomic Resolution X-Ray Crystal Structure of a Ruthenocene Conjug... -

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Basic information

Entry
Database: PDB / ID: 4xxr
TitleAtomic Resolution X-Ray Crystal Structure of a Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with CTX-M-14 E166A Beta-Lactamase
ComponentsCTX-M-14 Class A Beta-Lactamase
KeywordsHYDROLASE/ANTIBIOTIC / Beta-Lactamase Organometallic Ruthenocene CTX-M-14 / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JSC / Chem-JSD / Chem-JSE / : / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsLewandowski, E.M. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI 103158 United States
CitationJournal: Chem.Commun.(Camb.) / Year: 2015
Title: Antibacterial properties and atomic resolution X-ray complex crystal structure of a ruthenocene conjugated beta-lactam antibiotic.
Authors: Lewandowski, E.M. / Skiba, J. / Torelli, N.J. / Rajnisz, A. / Solecka, J. / Kowalski, K. / Chen, Y.
History
DepositionJan 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Mar 9, 2016Group: Experimental preparation
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CTX-M-14 Class A Beta-Lactamase
B: CTX-M-14 Class A Beta-Lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,10610
Polymers55,8852
Non-polymers3,2218
Water10,827601
1
A: CTX-M-14 Class A Beta-Lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0926
Polymers27,9431
Non-polymers2,1495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CTX-M-14 Class A Beta-Lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0154
Polymers27,9431
Non-polymers1,0723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.899, 106.775, 47.903
Angle α, β, γ (deg.)90.00, 101.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CTX-M-14 Class A Beta-Lactamase


Mass: 27942.512 Da / Num. of mol.: 2 / Fragment: UNP residues 29-291 / Mutation: E166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaCTX-M-14, beta-lactamase CTX-M-14, bla-CTX-M-14a, blaCTX-M-14a, blaCTX-M-14b, blaCTX-M-14c, blaCTX-M-27b, blatoho-3, blaUOE-2, CTX-M-14, ETN48_p0088, pCT_085, pHK01_011
Production host: Escherichia coli (E. coli) / References: UniProt: Q9L5C7, beta-lactamase

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Non-polymers , 5 types, 609 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-JSD / [(1,2,3,4,5-eta)-1-(4-{[(4-carboxy-5,5-dimethyl-1,3-thiazolidin-2-yl)methyl]amino}-4-oxobutanoyl)cyclopentadienyl][(1,2,3,4,5-eta)-cyclopentadienyl]ruthenium


Mass: 494.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H17N2O4RuS
#4: Chemical ChemComp-JSC / [(1,2,3,4,5-eta)-1-(4-{[carboxy(4-carboxy-5,5-dimethyl-1,3-thiazolidin-2-yl)methyl]amino}-4-oxobutanoyl)cyclopentadienyl][(1,2,3,4,5-eta)-cyclopentadienyl]ruthenium


Mass: 538.515 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C22H17N2O6RuS
#5: Chemical ChemComp-JSE / [(1,2,3,4,5-eta)-1-(4-{[carboxy(4-carboxy-5,5-dimethyl-1,3-thiazolidin-2-yl)methyl]amino}-4-oxobutanoyl)cyclopentadienyl][(1,2,3,4,5-eta)-cyclopentadienyl]ruthenium


Mass: 538.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C22H17N2O6RuS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 141750 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.54
Reflection shellResolution: 1.18→1.2 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.15 / Num. measured obs: 6158 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2P74

2p74


Resolution: 1.18→46.92 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.032 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15287 7105 5 %RANDOM
Rwork0.12493 ---
obs0.12633 134602 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.439 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0.09 Å2
2---0.25 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.18→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 146 601 4638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194793
X-RAY DIFFRACTIONr_bond_other_d0.0050.024530
X-RAY DIFFRACTIONr_angle_refined_deg1.38326534
X-RAY DIFFRACTIONr_angle_other_deg2.208310413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65224.359195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43915786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2671540
X-RAY DIFFRACTIONr_chiral_restr0.0870.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.0215745
X-RAY DIFFRACTIONr_gen_planes_other0.040.021103
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr16.02439323
X-RAY DIFFRACTIONr_sphericity_free41.7585127
X-RAY DIFFRACTIONr_sphericity_bonded10.60959624
LS refinement shellResolution: 1.18→1.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 438 -
Rwork0.182 8492 -
obs--83.9 %

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