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- PDB-4kz9: Crystal structure of AmpC beta-lactamase in complex with fragment... -

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Basic information

Entry
Database: PDB / ID: 4kz9
TitleCrystal structure of AmpC beta-lactamase in complex with fragment 41 ((4R,4aS,8aS)-4-phenyldecahydroquinolin-4-ol)
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
(4R,4aS,8aS)-4-phenyldecahydroquinolin-4-ol / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsEidam, O. / Barelier, S. / Fish, I. / Shoichet, B.K.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Increasing chemical space coverage by combining empirical and computational fragment screens.
Authors: Barelier, S. / Eidam, O. / Fish, I. / Hollander, J. / Figaroa, F. / Nachane, R. / Irwin, J.J. / Shoichet, B.K. / Siegal, G.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 20, 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)79,6926
Polymers79,1762
Non-polymers5164
Water16,952941
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1045
Polymers39,5881
Non-polymers5164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)39,5881
Polymers39,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.580, 76.420, 97.500
Angle α, β, γ (deg.)90.000, 115.700, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / / AmpC beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2 / Fragment: UNP residues 20-377
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.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-1U7 / (4R,4aS,8aS)-4-phenyldecahydroquinolin-4-ol


Mass: 231.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 941 / 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: 51.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 1.7 M potassium phosphate, pH 8.8, 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: May 24, 2012
RadiationMonochromator: KHOZU 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: 1.72→29.518 Å / Num. obs: 80298 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.734 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.72-1.760.5042.5718764583494.9
1.76-1.810.3923.2718302567395.1
1.81-1.870.3343.8617909554795.2
1.87-1.920.2595.3416801530894.5
1.92-1.990.225.8916855524295.3
1.99-2.060.1528.2116415509096.1
2.06-2.130.11910.2915865494896.2
2.13-2.220.11111.3415083472696.1
2.22-2.320.09513.8213736449694.8
2.32-2.430.07515.8314197442397.1
2.43-2.560.06218.1713321416297.2
2.56-2.720.05420.0512767399597.5
2.72-2.910.04424.1911892373097.8
2.91-3.140.03330.3311086350397.8
3.14-3.440.02636.5310099321897.9
3.44-3.850.02440.848755290696.9
3.85-4.440.0247.298173260298
4.44-5.440.01949.357102221798.6
5.44-7.690.02145.555505172899.1
7.690.01955.3291395096.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KE4

1ke4


Resolution: 1.72→29.518 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8775 / SU ML: 0.16 / σ(F): 1.99 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1925 2947 3.67 %
Rwork0.1543 --
obs0.1557 80291 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.24 Å2 / Biso mean: 20.3212 Å2 / Biso min: 5.96 Å2
Refinement stepCycle: LAST / Resolution: 1.72→29.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5460 0 32 941 6433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135676
X-RAY DIFFRACTIONf_angle_d1.4567786
X-RAY DIFFRACTIONf_chiral_restr0.098855
X-RAY DIFFRACTIONf_plane_restr0.008999
X-RAY DIFFRACTIONf_dihedral_angle_d12.572008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.74820.21261260.19533582370895
1.7482-1.77830.21991420.1863605374795
1.7783-1.81070.23521410.18413643378495
1.8107-1.84550.22541310.18423624375595
1.8455-1.88320.23011180.18943634375295
1.8832-1.92410.28271120.2543592370494
1.9241-1.96880.21141320.18173645377795
1.9688-2.01810.21261280.16133699382796
2.0181-2.07260.17371430.1513670381396
2.0726-2.13360.1911510.15883633378496
2.1336-2.20240.20781660.1573665383197
2.2024-2.28110.28261110.20293606371794
2.2811-2.37240.20191270.15613726385397
2.3724-2.48030.1781460.14893703384997
2.4803-2.6110.21291460.1473710385698
2.611-2.77450.19341550.15283721387698
2.7745-2.98850.19371640.1533707387198
2.9885-3.28890.18961540.14493751390598
3.2889-3.7640.14651380.12483780391898
3.764-4.73910.14231730.11283752392598
4.7391-29.52270.1961430.14943896403999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7070.5071-0.29131.7296-0.30821.82580.0707-0.24370.0040.3076-0.04760.16350.159-0.1057-0.02480.1756-0.03530.03370.1037-0.01470.106718.8317-10.829826.4698
21.11980.158-0.18462.5933-0.38231.5025-0.02530.18480.0477-0.21780.0261-0.0709-0.00030.0828-0.00170.0596-0.00720.00080.11280.00010.081639.81156.95358.1584
31.69141.0455-0.00341.54830.17780.99240.077-0.16920.00150.2459-0.0733-0.04080.09030.0410.0010.11850.0107-0.00760.08230.00440.08831.5386-2.257522.66
41.2911-0.7973-0.69022.36530.50452.3961-0.0398-0.0211-0.1361-0.05160.0086-0.0920.29270.24760.02730.110.0380.01080.1190.00810.117484.787-13.436821.6798
50.82970.0792-0.16412.50990.01221.58230.0083-0.2080.03780.24480.02950.0537-0.0918-0.0001-0.03540.0779-0.00850.00470.1182-0.00210.071564.81229.890835.9713
61.0422-0.8492-0.11071.5542-0.39041.4627-0.0020.0082-0.0285-0.07480.0146-0.00960.1250.0548-0.00750.0729-0.024-0.00390.0842-0.010.085472.634-3.412423.7585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:66)A4 - 66
2X-RAY DIFFRACTION2(chain A and resid 67:182)A67 - 182
3X-RAY DIFFRACTION3(chain A and resid 183:361)A183 - 361
4X-RAY DIFFRACTION4(chain B and resid 4:66)B4 - 66
5X-RAY DIFFRACTION5(chain B and resid 67:177)B67 - 177
6X-RAY DIFFRACTION6(chain B and resid 178:361)B178 - 361

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