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- PDB-3p09: Crystal Structure of Beta-Lactamase from Francisella tularensis -

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Basic information

Entry
Database: PDB / ID: 3p09
TitleCrystal Structure of Beta-Lactamase from Francisella tularensis
ComponentsBeta-lactamase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta sandwich / cytosol
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 speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.898 Å
AuthorsKim, Y. / Makowska-Grzyska, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Beta-Lactamase from Francisella tularensis
Authors: Kim, Y. / Makowska-Grzyska, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionSep 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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)65,62510
Polymers64,8612
Non-polymers7658
Water6,792377
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9116
Polymers32,4301
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7154
Polymers32,4301
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Beta-lactamase
B: Beta-lactamase
hetero molecules

A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,25120
Polymers129,7224
Non-polymers1,52916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6410 Å2
ΔGint-191 kcal/mol
Surface area43210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.652, 143.466, 46.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-354-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 32430.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_0611c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q5NH60, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25 % w/v Polyehtlyene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 41541 / Num. obs: 41541 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 23.35 Å2 / Rsym value: 0.095 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 1728 / Rsym value: 0.671 / % possible all: 83.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.898→40.72 Å / SU ML: 0.22 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2000 4.94 %random
Rwork0.162 ---
all0.164 40513 --
obs0.164 40513 95.69 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.663 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.163 Å20 Å20 Å2
2--4.5857 Å2-0 Å2
3---0.5774 Å2
Refinement stepCycle: LAST / Resolution: 1.898→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4165 0 41 377 4583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074327
X-RAY DIFFRACTIONf_angle_d1.0245874
X-RAY DIFFRACTIONf_dihedral_angle_d12.6671606
X-RAY DIFFRACTIONf_chiral_restr0.073657
X-RAY DIFFRACTIONf_plane_restr0.004759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8978-1.96570.28281570.23923027318476
1.9657-2.04440.26361940.19793719391394
2.0444-2.13740.24971980.17053827402596
2.1374-2.25010.20081990.15843823402297
2.2501-2.3910.24832020.16213912311498
2.391-2.57560.23162060.17673942314899
2.5756-2.83480.23112040.16943947315198
2.8348-3.24480.21532080.16884006421499
3.2448-4.08750.16332110.145740654276100
4.0875-40.72890.18972210.15024245446699
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)
11.5213-0.51390.57570.9726-0.27071.0598-0.05620.0155-0.00340.05280.03160.0134-0.1104-0.02860.0190.11630.00510.0120.123-0.01270.120524.349180.091318.8929
21.3563-0.36820.37821.0607-0.71121.79220.05940.09230.05250.02860.08090.0408-0.2569-0.0905-0.12410.1450.01820.04150.11560.04460.1212-8.41996.09887.8128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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