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- PDB-4d2o: Crystal structure of the class A extended-spectrum beta-lactamase... -

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Basic information

Entry
Database: PDB / ID: 4d2o
TitleCrystal structure of the class A extended-spectrum beta-lactamase PER- 2
ComponentsPER-2 BETA-LACTAMASE
KeywordsHYDROLASE / OXYIMINO-CEPHALOSPORINASE / ESBL / CEFOTAXIMASE
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 speciesCITROBACTER FREUNDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPower, P. / Herman, R. / Ruggiero, M. / Kerff, F. / Galleni, M. / Gutkind, G. / Charlier, P. / Sauvage, E.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2014
Title: Crystal Structure of the Extended-Spectrum Beta-Lactamase Per- 2 and Insights Into the Role of Specific Residues in the Interaction with Beta-Lactams and Beta-Lactamase Inhibitors.
Authors: Ruggiero, M. / Sauvage, E. / Herman, R. / Galleni, M. / Gutkind, G. / Charlier, P. / Power, P.
History
DepositionMay 12, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionMay 21, 2014ID: 3ZNW
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PER-2 BETA-LACTAMASE
B: PER-2 BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)61,9132
Polymers61,9132
Non-polymers00
Water2,738152
1
A: PER-2 BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)30,9561
Polymers30,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PER-2 BETA-LACTAMASE


Theoretical massNumber of molelcules
Total (without water)30,9561
Polymers30,9561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.480, 83.880, 68.944
Angle α, β, γ (deg.)90.00, 103.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PER-2 BETA-LACTAMASE / CLASS A BETA-LACTAMASE


Mass: 30956.328 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A2RP81, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 1.89 Å3/Da / Density % sol: 34.3 % / Description: NONE
Crystal growDetails: 0.1 M HEPES, 1.5 M SODIUM CITRATE BUFFER (PH 7.5).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.2→41.94 Å / Num. obs: 23354 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E25

1e25


Resolution: 2.2→33.46 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.878 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23969 1199 5.1 %RANDOM
Rwork0.19442 ---
obs0.19676 22125 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2---0.07 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 0 152 4407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9555830
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43526.243181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18515759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7931510
X-RAY DIFFRACTIONr_chiral_restr0.1050.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213126
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 88 -
Rwork0.267 1574 -
obs--99.94 %
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)
10.9787-0.2750.46460.6975-0.46010.9712-0.0115-0.03650.0340.1161-0.0135-0.1161-0.01740.0350.0250.11780.00140.00990.1454-0.01770.044113.012-17.41241.102
20.6162-0.28210.52940.88930.38822.2590.01020.05170.0508-0.0633-0.065-0.0663-0.10750.01260.05480.08990.0060.03470.13820.01230.08387.153-4.84221.26
32.55690.9182-2.01072.5433-3.0014.27470.00290.0998-0.01410.0904-0.0824-0.1687-0.05230.08820.07950.1152-0.0001-0.06190.1344-0.00270.1220.079-4.48631.433
40.22-0.25860.16570.8792-0.20530.5359-0.03030.00170.00240.01910.01310.0498-0.022-0.04030.01720.082-0.00350.03580.16280.00510.07747.453-17.00733.701
55.84381.1321-1.60611.4738-0.72191.34640.01040.13130.1015-0.09830.0108-0.04130.07940.0326-0.02130.08340.00670.01720.13730.00790.072415.722-22.2435.187
66.38242.5426-3.7591.855-2.16264.0415-0.0821-0.0501-0.2498-0.12180.0182-0.09490.2861-0.07260.06390.14120.0159-0.02020.13520.00820.076511.447-32.3640.093
70.34370.11730.16440.4495-0.121.49110.01340.0010.003-0.136-0.02130.033-0.0313-0.06910.00790.0980.001-0.00390.1421-0.01890.0762-9.956-22.489-0.809
82.38240.36660.42862.4514-0.67121.93560.10.0521-0.1445-0.0805-0.0707-0.1601-0.04870.1413-0.02930.1003-0.00650.02410.1447-0.00280.04879.973-31.78416.24
92.4018-0.15270.15461.6687-0.18461.91170.05610.0799-0.0609-0.11040.0134-0.05860.1735-0.0201-0.06960.11270.0041-0.01880.1101-0.02960.0404-2.832-33.1740.81
100.99790.1509-0.01121.319-0.7460.9742-0.0221-0.0107-0.06960.0672-0.0151-0.0087-0.0745-0.07610.03730.08230.01050.01640.1538-0.02640.0711-4.277-19.9559.184
111.96050.2414-1.57140.69110.20523.0227-0.0693-0.07980.0149-0.06740.02160.08770.08170.07530.04770.09070.02430.00670.1118-0.00240.0985-7.892-16.0091.542
1213.0252-1.2389-4.13771.02980.10521.9605-0.06770.25220.33750.04290.08910.0332-0.0992-0.2245-0.02140.17190.0415-0.02410.14120.01330.0464-13.492-9.4291.853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 89
2X-RAY DIFFRACTION2A90 - 156
3X-RAY DIFFRACTION3A157 - 174
4X-RAY DIFFRACTION4A175 - 239
5X-RAY DIFFRACTION5A240 - 272
6X-RAY DIFFRACTION6A273 - 297
7X-RAY DIFFRACTION7B26 - 87
8X-RAY DIFFRACTION8B88 - 137
9X-RAY DIFFRACTION9B138 - 195
10X-RAY DIFFRACTION10B196 - 251
11X-RAY DIFFRACTION11B252 - 272
12X-RAY DIFFRACTION12B273 - 297

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