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- PDB-2hdu: AmpC beta-lactamase in complex with 2-acetamidothiophene-3-carbox... -

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Basic information

Entry
Database: PDB / ID: 2hdu
TitleAmpC beta-lactamase in complex with 2-acetamidothiophene-3-carboxylic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / AmpC beta-lactamase fragment-based drug design
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / 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
2-(ACETYLAMINO)THIOPHENE-3-CARBOXYLIC ACID / : / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 1.3Oct 18, 2017Group: Refinement description / Category: software

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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)80,79212
Polymers79,1762
Non-polymers1,61610
Water17,330962
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9583
Polymers39,5881
Non-polymers3702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8339
Polymers39,5881
Non-polymers1,2458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.905, 77.057, 97.520
Angle α, β, γ (deg.)90.000, 116.860, 90.000
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-F12 / 2-(ACETYLAMINO)THIOPHENE-3-CARBOXYLIC ACID


Mass: 185.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H7NO3S
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 962 / 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: 50.68 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 2.8 % / Av σ(I) over netI: 14.6 / Number: 355860 / Rmerge(I) obs: 0.042 / Χ2: 1 / D res high: 1.49 Å / D res low: 50 Å / Num. obs: 126514 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.215098.410.0271.6082.8
2.553.2199.810.0311.2982.9
2.232.5510010.0371.1732.9
2.022.2310010.0471.152.9
1.882.0210010.0650.9992.9
1.771.8810010.0940.8162.8
1.681.7710010.1380.7512.8
1.611.6810010.1910.7082.8
1.541.6110010.2570.6852.8
1.491.5499.510.3590.6782.6
ReflectionResolution: 1.49→50 Å / Num. all: 126514 / Num. obs: 126514 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.042 / Χ2: 0.996 / Net I/σ(I): 14.6
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.3 / Num. unique all: 12573 / Χ2: 0.678 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→87.04 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.061 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.168 6318 5 %RANDOM
Rwork0.135 ---
obs0.136 126514 99.5 %-
all-126505 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.26 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.49→87.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5897 0 114 967 6978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226211
X-RAY DIFFRACTIONr_bond_other_d0.0010.024151
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9648557
X-RAY DIFFRACTIONr_angle_other_deg1.019310211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17324.764275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.873151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3581529
X-RAY DIFFRACTIONr_chiral_restr0.1240.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021243
X-RAY DIFFRACTIONr_nbd_refined0.2410.21370
X-RAY DIFFRACTIONr_nbd_other0.2020.24437
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23019
X-RAY DIFFRACTIONr_nbtor_other0.0880.22981
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2674
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.254
X-RAY DIFFRACTIONr_mcbond_it1.4171.53725
X-RAY DIFFRACTIONr_mcbond_other0.6371.51485
X-RAY DIFFRACTIONr_mcangle_it2.11726080
X-RAY DIFFRACTIONr_scbond_it2.95532561
X-RAY DIFFRACTIONr_scangle_it4.1414.52427
X-RAY DIFFRACTIONr_rigid_bond_restr1.418310610
X-RAY DIFFRACTIONr_sphericity_free7.2353955
X-RAY DIFFRACTIONr_sphericity_bonded3.34310149
LS refinement shellResolution: 1.49→1.528 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 423 -
Rwork0.171 8627 -
obs-9050 96.16 %

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