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- PDB-3tsg: Crystal structure of GES-14 -

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Basic information

Entry
Database: PDB / ID: 3tsg
TitleCrystal structure of GES-14
ComponentsExtended-spectrum beta-lactamase GES-14
KeywordsHYDROLASE / Beta lactamase fold / beta lactams
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
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
IODIDE ION / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDelbruck, H. / Hoffmann, K.M.V. / Bebrone, C.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2012
Title: Kinetic and crystallographic studies of extended-spectrum GES-11, GES-12, and GES-14 beta-lactamases.
Authors: Delbruck, H. / Bogaerts, P. / Kupper, M.B. / Rezende de Castro, R. / Bennink, S. / Glupczynski, Y. / Galleni, M. / Hoffmann, K.M. / Bebrone, C.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 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: Extended-spectrum beta-lactamase GES-14
B: Extended-spectrum beta-lactamase GES-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46668
Polymers62,4732
Non-polymers7,99366
Water5,044280
1
A: Extended-spectrum beta-lactamase GES-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,41235
Polymers31,2361
Non-polymers4,17534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extended-spectrum beta-lactamase GES-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,05433
Polymers31,2361
Non-polymers3,81732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.745, 84.098, 85.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Extended-spectrum beta-lactamase GES-14


Mass: 31236.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: blaGES-14 / Plasmid: pet28a/blaGES-14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3X610, beta-lactamase
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na iodide, 30 % PEG 3350, 5 % Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2011 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.61 Å / Num. all: 40716 / Num. obs: 40657 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.124 / Net I/σ(I): 11.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 5838 / Rsym value: 0.608 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QPN
Resolution: 1.9→19.61 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.9 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20473 2042 5 %RANDOM
Rwork0.16314 ---
all0.16525 40716 --
obs0.16525 38560 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.629 Å2
Baniso -1Baniso -2Baniso -3
1--3.07 Å20 Å20 Å2
2--2.78 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4060 0 121 280 4461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224428
X-RAY DIFFRACTIONr_bond_other_d0.0010.023102
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9746025
X-RAY DIFFRACTIONr_angle_other_deg0.86537588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51923.692195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42615789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9841540
X-RAY DIFFRACTIONr_chiral_restr0.0690.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02895
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3631.52748
X-RAY DIFFRACTIONr_mcbond_other0.0961.51124
X-RAY DIFFRACTIONr_mcangle_it0.64724458
X-RAY DIFFRACTIONr_scbond_it1.1931680
X-RAY DIFFRACTIONr_scangle_it1.9024.51529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 133 -
Rwork0.212 2784 -
obs-2784 99.97 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.07280.07981.44250.7496-0.07892.8298-0.06970.13590.1557-0.0886-0.02280.1262-0.093-0.08260.09250.25530.0083-0.02040.12250.01090.166630.92823.5153.339
21.2294-0.56670.38420.7268-0.37930.54710.0665-0.2005-0.12990.04080.02670.0190.0657-0.1053-0.09320.282-0.0156-0.00390.09270.02210.143350.7019.38920.196
32.9330.14060.39690.3955-0.13520.52920.0666-0.072-0.23090.0293-0.01290.01780.1072-0.1487-0.05370.27720.0042-0.02640.04790.01990.147158.0068.26618.06
44.9007-1.6685-0.19833.29562.17924.28970.145-0.2049-0.368-0.0538-0.00440.18110.1653-0.1022-0.14070.2891-0.0336-0.03860.0590.06910.199339.6065.23216.209
51.93580.22310.51740.5555-0.18120.7657-0.0071-0.11760.13070.0291-0.03940.0511-0.0356-0.04270.04650.2270.002-0.01450.0632-0.0040.121744.77521.89515.122
63.5874-1.0552-1.03974.42422.99776.56080.0321-0.14110.3456-0.0667-0.04660.044-0.2905-0.04470.01450.18670.0043-0.03750.07750.02260.14241.82124.51610.193
72.5978-0.27530.41512.13270.83433.0459-0.01140.37410.1889-0.2479-0.0341-0.0072-0.0250.19610.04550.2147-0.008-0.03360.13360.02390.097839.94222.2930.839
84.0416-3.15552.14286.3786-4.05291.78170.25530.5977-0.0565-0.1559-0.3515-0.19420.08110.24480.09630.33450.03080.0210.173-0.06070.143591.4229.546-1.325
92.29440.3981-0.87351.6621-0.32292.24090.05010.03790.1841-0.0406-0.1119-0.17480.12860.20730.06180.27870.0037-0.0040.0382-0.02860.199588.29818.8211.029
101.0117-0.0481-1.96812.420.26314.6021-0.0503-0.29530.20090.40080.1789-0.1622-0.1455-0.0047-0.12870.34780.0652-0.04890.1319-0.06410.232172.90829.25224.684
112.7277-0.7709-0.1212.4011.52751.85540.05040.10340.2265-0.1782-0.02750.10910.0189-0.1509-0.0230.2715-0.0123-0.00470.02610.00780.188162.19735.02613.379
122.2302-0.44650.42180.65910.26470.2573-0.04430.06090.16780.01960.0443-0.0257-0.00170.041400.27530.0068-0.00460.015-0.01210.156666.73531.27515.095
133.3555-0.74771.68133.1348-0.49824.4930.09560.20110.2061-0.27110.0279-0.3121-0.07170.235-0.12350.27990.00110.03410.0177-0.00890.266182.71432.9179.255
141.6181-0.1844-0.03251.2140.20030.72080.02670.0429-0.0089-0.0521-0.0262-0.04680.04530.0003-0.00050.2360.0081-0.00580.0154-0.0060.134779.01114.34111.668
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 56
2X-RAY DIFFRACTION2A57 - 99
3X-RAY DIFFRACTION3A100 - 140
4X-RAY DIFFRACTION4A141 - 172
5X-RAY DIFFRACTION5A173 - 232
6X-RAY DIFFRACTION6A233 - 250
7X-RAY DIFFRACTION7A251 - 284
8X-RAY DIFFRACTION8B20 - 38
9X-RAY DIFFRACTION9B39 - 66
10X-RAY DIFFRACTION10B67 - 84
11X-RAY DIFFRACTION11B85 - 99
12X-RAY DIFFRACTION12B100 - 146
13X-RAY DIFFRACTION13B147 - 174
14X-RAY DIFFRACTION14B175 - 284

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