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

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Basic information

Entry
Database: PDB / ID: 1yms
TitleX-ray crystallographic structure of CTX-M-9 beta-lactamase complexed with nafcinin-like boronic acid inhibitor
Componentsbeta-lactamase CTX-M-9
KeywordsHYDROLASE / CTX-M / beta-lactamase / transition state / acylation
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
[(2-ETHOXY-1-NAPHTHOYL)AMINO]METHYLBORONIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 21, 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)56,4914
Polymers55,9452
Non-polymers5462
Water14,484804
1
A: beta-lactamase CTX-M-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2462
Polymers27,9721
Non-polymers2731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase CTX-M-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2462
Polymers27,9721
Non-polymers2731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.260, 106.825, 47.867
Angle α, β, γ (deg.)90.00, 101.74, 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: CTX-M-9 beta-lactamase, V231A / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical ChemComp-NBF / [(2-ETHOXY-1-NAPHTHOYL)AMINO]METHYLBORONIC ACID


Mass: 273.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16BNO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.02 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 / Wavelength: 1.11587 Å
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: 1.6→22 Å / Num. all: 58748 / Num. obs: 57897 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.22 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.48 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YLJ

1ylj


Resolution: 1.6→19.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 81987.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ONLY 5 ATOMS WERE MODELED FOR A25 GLN with the side chain truncated after CB
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2820 5.1 %RANDOM
Rwork0.157 ---
obs0.157 55531 94.7 %-
all-58748 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.3739 Å2 / ksol: 0.36281 e/Å3
Displacement parametersBiso mean: 10.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å21.13 Å2
2---0.81 Å20 Å2
3---1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.6→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 40 804 4793
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.392.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 413 4.8 %
Rwork0.212 8206 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM_SNAPROTEIN.TOP_SNA
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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