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- PDB-5vle: Ultrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conju... -

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Basic information

Entry
Database: PDB / ID: 5vle
TitleUltrahigh Resolution X-Ray Crystal Structure of Ruthenocene Conjugated Penicilloate and Penilloate Products in Complex with CTX-M-14 E166A Beta-Lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-Lactamase / organometallic / Ruthenocene / CTX-M-14
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 / : / PHOSPHATE ION / RUTHENIUM ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.85 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)AI03158 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
DepositionApr 25, 2017Deposition 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 2.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,22412
Polymers55,8512
Non-polymers3,37310
Water12,016667
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1327
Polymers27,9251
Non-polymers2,2066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0935
Polymers27,9251
Non-polymers1,1674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.745, 106.418, 47.611
Angle α, β, γ (deg.)90.00, 102.38, 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


Mass: 27925.480 Da / Num. of mol.: 2 / Fragment: UNP residues 22-284 / Mutation: E166A
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 , 7 types, 677 molecules

#2: 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.: 3 / Source method: obtained synthetically / Formula: C21H17N2O4RuS
#3: 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
#4: 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
#5: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 101.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ru
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.95 %
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: 23-ID-B / Wavelength: 0.7 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2014
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.85→50 Å / Num. obs: 374335 / % possible obs: 98.7 % / Redundancy: 6.6 % / Net I/σ(I): 45.77
Reflection shellResolution: 0.85→0.86 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.25 / Num. unique obs: 17884 / % possible all: 94.2

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Processing

Software
NameClassification
SHELXL-97refinement
SHELXphasing
SCALEPACKdata scaling
HKL-2000data reduction
RefinementResolution: 0.85→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
all0.109 ---
obs-320421 98.7 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 225 / Occupancy sum hydrogen: 3758.1 / Occupancy sum non hydrogen: 4594.4
Refinement stepCycle: 1 / Resolution: 0.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 170 668 4737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.033
X-RAY DIFFRACTIONs_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.07
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.032
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellHighest resolution: 0.85 Å

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