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- PDB-1yly: X-ray crystallographic structure of CTX-M-9 beta-lactamase comple... -

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Basic information

Entry
Database: PDB / ID: 1yly
TitleX-ray crystallographic structure of CTX-M-9 beta-lactamase complexed with ceftazidime-like boronic acid
Componentsbeta-lactamase CTX-M-9
KeywordsHYDROLASE / CTX-M / beta-lactamase / transition state / ceftazidime / boronic acid
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic / metal ion binding
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-CB4 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.25 Å
AuthorsChen, Y. / Shoichet, B. / Bonnet, R.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Structure, Function, and Inhibition along the Reaction Coordinate of CTX-M beta-Lactamases.
Authors: Chen, Y. / Shoichet, B. / Bonnet, R.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: beta-lactamase CTX-M-9
B: beta-lactamase CTX-M-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7956
Polymers55,9452
Non-polymers8504
Water15,637868
1
A: beta-lactamase CTX-M-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3032
Polymers27,9721
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase CTX-M-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4934
Polymers27,9721
Non-polymers5203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.182, 106.845, 47.882
Angle α, β, γ (deg.)90.00, 101.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein beta-lactamase CTX-M-9


Mass: 27972.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M / Plasmid: pET-9a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Keywords: V231A, CTX-M-9 beta-lactamase / References: UniProt: Q9L5C7, beta-lactamase
#2: Chemical ChemComp-CB4 / PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE


Mass: 330.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15BN4O6S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / Source method: isolated from a natural source / Formula: H2O
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: 1.7 Å3/Da / Density % sol: 27.8 %
Crystal growTemperature: 293 K / pH: 8.8
Details: potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2004 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.25→22 Å / Num. obs: 113478 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 5.22 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 15.9
Reflection shellResolution: 1.25→1.29 Å / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 2.13 / % possible all: 76.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: 1YLJ

1ylj


Resolution: 1.25→22 Å / Num. parameters: 46266 / Num. restraintsaints: 58260 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT. RIDING HYDROGENS INCLUDED IN REFINEMENT. WATER MOLECULES IN CLOSE CONTACT HAVE A COMBINED OCCUPANCY OF 1.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 5637 5.2 %RANDOM
Rwork0.129 ---
all0.129 107782 --
obs0.129 107782 88.1 %-
Refine analyzeNum. disordered residues: 78 / Occupancy sum hydrogen: 3767.97 / Occupancy sum non hydrogen: 4751.18
Refinement stepCycle: LAST / Resolution: 1.25→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 54 868 5135
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.036
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.047
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.014
X-RAY DIFFRACTIONs_approx_iso_adps0.051

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