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- PDB-4okp: Crystal structure of AmpC beta-lactamase in complex with the prod... -

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Basic information

Entry
Database: PDB / ID: 4okp
TitleCrystal structure of AmpC beta-lactamase in complex with the product form of 7-amino-desacetoxycephalosporanic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / AMPC BETA-LACTAMASE / CLASS C / CEPHALOSPORINASE
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
Chem-2V0 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsBarelier, S.B. / Shoichet, B.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Substrate deconstruction and the nonadditivity of enzyme recognition.
Authors: Barelier, S. / Cummings, J.A. / Rauwerdink, A.M. / Hitchcock, D.S. / Farelli, J.D. / Almo, S.C. / Raushel, F.M. / Allen, K.N. / Shoichet, B.K.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)79,5985
Polymers79,1762
Non-polymers4223
Water14,628812
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7783
Polymers39,5881
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8202
Polymers39,5881
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.120, 76.490, 97.620
Angle α, β, γ (deg.)90.00, 115.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2 / Fragment: Beta-lactamase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-2V0 / (2R)-2-[(R)-amino(carboxy)methyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / 7-aminodeacetoxycephalosporanic acid, hydrolyzed form


Mass: 232.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 1.7 M POTASSIUM PHOSPHATE, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2012
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.37→30 Å / Num. all: 163866 / Num. obs: 161772 / % possible obs: 98.7 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.37→1.45 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→29.284 Å / SU ML: 0.35 / σ(F): 1.99 / Phase error: 14.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1645 6203 3.83 %
Rwork0.1428 --
obs0.1437 161759 98.84 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.275 Å2 / ksol: 0.419 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9126 Å2-0 Å2-1.1171 Å2
2---2.4337 Å20 Å2
3---0.5211 Å2
Refinement stepCycle: LAST / Resolution: 1.37→29.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5463 0 25 812 6300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055949
X-RAY DIFFRACTIONf_angle_d1.1268200
X-RAY DIFFRACTIONf_dihedral_angle_d11.4762139
X-RAY DIFFRACTIONf_chiral_restr0.07892
X-RAY DIFFRACTIONf_plane_restr0.0061080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3703-1.38590.2911980.23564766X-RAY DIFFRACTION92
1.3859-1.40220.23472150.20555149X-RAY DIFFRACTION99
1.4022-1.41930.23652140.195143X-RAY DIFFRACTION98
1.4193-1.43730.21982150.17545161X-RAY DIFFRACTION99
1.4373-1.45620.20852150.16735162X-RAY DIFFRACTION99
1.4562-1.47610.20622170.15895192X-RAY DIFFRACTION99
1.4761-1.49720.16632170.14725221X-RAY DIFFRACTION99
1.4972-1.51950.17942150.13145145X-RAY DIFFRACTION99
1.5195-1.54330.1732150.1285162X-RAY DIFFRACTION99
1.5433-1.56860.16482180.12655229X-RAY DIFFRACTION99
1.5686-1.59560.1732150.1225166X-RAY DIFFRACTION99
1.5956-1.62460.17512160.12755201X-RAY DIFFRACTION100
1.6246-1.65590.15672180.1225214X-RAY DIFFRACTION100
1.6559-1.68970.1572150.1195174X-RAY DIFFRACTION100
1.6897-1.72640.15441920.11235255X-RAY DIFFRACTION100
1.7264-1.76660.14981950.11695237X-RAY DIFFRACTION100
1.7666-1.81080.14482160.11455222X-RAY DIFFRACTION100
1.8108-1.85970.15581880.12175239X-RAY DIFFRACTION100
1.8597-1.91440.14261610.12455299X-RAY DIFFRACTION100
1.9144-1.97620.16611900.13085200X-RAY DIFFRACTION100
1.9762-2.04680.1531860.13595259X-RAY DIFFRACTION100
2.0468-2.12870.14422210.1365260X-RAY DIFFRACTION100
2.1287-2.22560.15532040.13255197X-RAY DIFFRACTION99
2.2256-2.34290.14941970.13545242X-RAY DIFFRACTION99
2.3429-2.48960.17221920.14385252X-RAY DIFFRACTION100
2.4896-2.68170.18612110.15075234X-RAY DIFFRACTION100
2.6817-2.95130.17472290.16115247X-RAY DIFFRACTION99
2.9513-3.37790.16722110.15645229X-RAY DIFFRACTION99
3.3779-4.25370.12672150.13155211X-RAY DIFFRACTION98
4.2537-29.29070.1851920.16664888X-RAY DIFFRACTION91

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