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- PDB-5top: Atomic Resolution X-Ray Crystal Structure of a Ruthenocene Conjug... -

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Basic information

Entry
Database: PDB / ID: 5top
TitleAtomic Resolution X-Ray Crystal Structure of a Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with CTX-M-14 S70G Beta-Lactamase
ComponentsBeta-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
ruthenocene / Chem-JSC / Chem-JSE / : / RUTHENIUM ION / 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, Poland, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103158 United States
Polish National Science CentreDEC-2013/11/B/ST5/00997 Poland
CitationJournal: FEBS J. / Year: 2018
Title: Mechanisms of proton relay and product release by Class A beta-lactamase at ultrahigh resolution.
Authors: Lewandowski, E.M. / Lethbridge, K.G. / Sanishvili, R. / Skiba, J. / Kowalski, K. / Chen, Y.
History
DepositionOct 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 2.0Dec 11, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Oct 4, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,13511
Polymers55,9072
Non-polymers2,2289
Water10,413578
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1715
Polymers27,9531
Non-polymers1,2174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9646
Polymers27,9531
Non-polymers1,0115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.093, 106.821, 47.933
Angle α, β, γ (deg.)90.00, 101.66, 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 Beta-lactamase / CTX-M-14 Class A Beta-Lactamase


Mass: 27953.488 Da / Num. of mol.: 2 / Mutation: S70G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Production host: Escherichia coli (E. coli) / References: UniProt: H6UQI0, beta-lactamase

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Non-polymers , 6 types, 587 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: 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.: 2 / Source method: obtained synthetically / Formula: C22H17N2O6RuS
#4: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ru
#5: 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.: 1 / Source method: obtained synthetically / Formula: C22H17N2O6RuS
#6: Chemical ChemComp-7G4 / ruthenocene / bis[(1,2,3,4,5-eta)-cyclopentadienyl]ruthenium


Mass: 231.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10Ru
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.9 %
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: Apr 1, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: 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: 133593 / % possible obs: 97.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 25.8
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.3 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XXR

4xxr


Resolution: 1.18→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.942 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.035 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14633 7118 5.1 %RANDOM
Rwork0.12756 ---
obs0.12848 133593 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.55 Å2
2---0.47 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 112 578 4593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194731
X-RAY DIFFRACTIONr_bond_other_d0.0010.024477
X-RAY DIFFRACTIONr_angle_refined_deg1.3452.0016457
X-RAY DIFFRACTIONr_angle_other_deg0.687310292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9835630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42624.433194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34215775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8041539
X-RAY DIFFRACTIONr_chiral_restr0.0850.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215662
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021081
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_it0.4451.4732385
X-RAY DIFFRACTIONr_mcbond_other0.4451.4712383
X-RAY DIFFRACTIONr_mcangle_it0.6452.2193060
X-RAY DIFFRACTIONr_mcangle_other0.6452.2193061
X-RAY DIFFRACTIONr_scbond_it0.441.6652346
X-RAY DIFFRACTIONr_scbond_other0.441.6652343
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6132.4323363
X-RAY DIFFRACTIONr_long_range_B_refined1.7620.3235846
X-RAY DIFFRACTIONr_long_range_B_other1.7620.3235847
X-RAY DIFFRACTIONr_rigid_bond_restr3.37839208
X-RAY DIFFRACTIONr_sphericity_free25.0871141
X-RAY DIFFRACTIONr_sphericity_bonded6.60419488
LS refinement shellResolution: 1.18→1.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.177 457 -
Rwork0.162 8147 -
obs--80.23 %

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