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- PDB-2hdq: AmpC beta-lactamase in complex with 2-carboxythiophene -

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Basic information

Entry
Database: PDB / ID: 2hdq
TitleAmpC beta-lactamase in complex with 2-carboxythiophene
ComponentsBeta-lactamase
KeywordsHYDROLASE / Fragment-based beta-lactamase AmpC drug design
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOPHENE-2-CARBOXYLIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBabaoglu, K. / Shoichet, B.K.
CitationJournal: Nat.Chem.Biol. / Year: 2006
Title: Deconstructing fragment-based inhibitor discovery
Authors: Babaoglu, K. / Shoichet, B.K.
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)80,71414
Polymers79,1762
Non-polymers1,53812
Water8,755486
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3577
Polymers39,5881
Non-polymers7696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3577
Polymers39,5881
Non-polymers7696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.434, 74.781, 98.281
Angle α, β, γ (deg.)90.00, 116.14, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a monomer

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: ampC / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical
ChemComp-C21 / THIOPHENE-2-CARBOXYLIC ACID


Mass: 128.149 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H4O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 2.5 % / Av σ(I) over netI: 7.9 / Number: 101651 / Rmerge(I) obs: 0.089 / Χ2: 1.27 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 41267 / % possible obs: 91
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.525095.110.0481.9342.5
3.594.5296.610.0491.7922.5
3.143.5997.110.0621.3882.5
2.853.1497.210.1041.3172.5
2.652.8594.510.1511.1572.5
2.492.6591.510.1981.0322.5
2.372.498810.2541.052.6
2.262.378710.3040.9852.5
2.182.2684.210.320.9392.3
2.12.1878.510.3930.8562.2
ReflectionResolution: 2.1→50 Å / Num. obs: 69905 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.2 / % possible all: 78.5

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KE4

1ke4


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.963 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2085 5.1 %RANDOM
Rwork0.183 ---
obs0.183 41236 90.72 %-
all-41236 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.107 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20.48 Å2
2---0.03 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5600 0 96 486 6182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225837
X-RAY DIFFRACTIONr_bond_other_d0.0010.023862
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9627970
X-RAY DIFFRACTIONr_angle_other_deg0.99139429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02924.776245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61515895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1371522
X-RAY DIFFRACTIONr_chiral_restr0.0720.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
X-RAY DIFFRACTIONr_nbd_refined0.1930.21163
X-RAY DIFFRACTIONr_nbd_other0.1880.23850
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22768
X-RAY DIFFRACTIONr_nbtor_other0.0850.22820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2392
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.220
X-RAY DIFFRACTIONr_mcbond_it0.861.54576
X-RAY DIFFRACTIONr_mcbond_other0.1331.51436
X-RAY DIFFRACTIONr_mcangle_it0.96525766
X-RAY DIFFRACTIONr_scbond_it1.6232838
X-RAY DIFFRACTIONr_scangle_it2.3194.52204
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 137 -
Rwork0.228 2341 -
obs-2478 74.28 %

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