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- PDB-4rx2: A triple mutant in the omega-loop of TEM-1 beta-lactamase changes... -

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Basic information

Entry
Database: PDB / ID: 4rx2
TitleA triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE / globular / beta-lactamase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.315 Å
AuthorsStojanoski, V. / Chow, D. / Hu, L. / Sankaran, B. / Gilbert, H. / Prasad, B.V.V. / Palzkill, T.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Triple Mutant in the Omega-loop of TEM-1 beta-Lactamase Changes the Substrate Profile via a Large Conformational Change and an Altered General Base for Catalysis.
Authors: Stojanoski, V. / Chow, D.C. / Hu, L. / Sankaran, B. / Gilbert, H.F. / Prasad, B.V. / Palzkill, T.
History
DepositionDec 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Sep 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase TEM
B: Beta-lactamase TEM
C: Beta-lactamase TEM
D: Beta-lactamase TEM
E: Beta-lactamase TEM
F: Beta-lactamase TEM
G: Beta-lactamase TEM
H: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,83116
Polymers231,0638
Non-polymers7698
Water14,718817
1
A: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9792
Polymers28,8831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9792
Polymers28,8831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9792
Polymers28,8831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9792
Polymers28,8831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9792
Polymers28,8831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9792
Polymers28,8831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9792
Polymers28,8831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Beta-lactamase TEM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9792
Polymers28,8831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.320, 83.300, 95.920
Angle α, β, γ (deg.)90.06, 89.97, 90.02
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 26 - 288 / Label seq-ID: 1 - 261

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28882.865 Da / Num. of mol.: 8 / Fragment: TEM-1 beta-lactamase / Mutation: W165Y/E166Y/P167G/M182T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 817 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M HEPES pH6.5, 30% W/V PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2013
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.315→62.89 Å / Num. all: 21570 / Num. obs: 21750 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.315-2.40.4813.1199.3
8.98-48.870.0997.5199.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BTL

1btl


Resolution: 2.315→62.89 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.866 / SU B: 8.669 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.726 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26795 4081 5 %RANDOM
Rwork0.23501 ---
obs0.23667 76898 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.496 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.01 Å2-0.64 Å2
2---0.28 Å2-0.17 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.315→62.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15679 0 40 817 16536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916021
X-RAY DIFFRACTIONr_bond_other_d0.0080.0215567
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.97821681
X-RAY DIFFRACTIONr_angle_other_deg1.19335792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13352024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02423.407678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.308152835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.08315144
X-RAY DIFFRACTIONr_chiral_restr0.0830.22509
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02117918
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023470
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_it1.5822.0968156
X-RAY DIFFRACTIONr_mcbond_other1.5822.0968155
X-RAY DIFFRACTIONr_mcangle_it2.5553.13510160
X-RAY DIFFRACTIONr_mcangle_other2.5543.13510161
X-RAY DIFFRACTIONr_scbond_it1.622.2927865
X-RAY DIFFRACTIONr_scbond_other1.6192.2937833
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6783.3811473
X-RAY DIFFRACTIONr_long_range_B_refined5.44716.45219386
X-RAY DIFFRACTIONr_long_range_B_other5.3116.55619015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A167640.03
12B167640.03
21A167850.02
22C167850.02
31A168680.01
32D168680.01
41A167160.02
42E167160.02
51A166790.04
52F166790.04
61A164370.05
62G164370.05
71A164740.05
72H164740.05
81B168890.03
82C168890.03
91B168570.03
92D168570.03
101B166830.03
102E166830.03
111B166020.04
112F166020.04
121B163580.05
122G163580.05
131B163990.05
132H163990.05
141C168630.02
142D168630.02
151C166550.02
152E166550.02
161C166160.04
162F166160.04
171C163610.05
172G163610.05
181C164130.05
182H164130.05
191D167390.02
192E167390.02
201D166900.04
202F166900.04
211D164420.05
212G164420.05
221D164880.05
222H164880.05
231E165460.04
232F165460.04
241E162450.05
242G162450.05
251E163400.05
252H163400.05
261F162920.06
262G162920.06
271F164880.05
272H164880.05
281G161600.06
282H161600.06
LS refinement shellResolution: 2.315→2.376 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 314 -
Rwork0.223 5465 -
obs--96.69 %

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