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- PDB-6n1n: Crystal structure of class D beta-lactamase from Sebaldella termi... -

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Basic information

Entry
Database: PDB / ID: 6n1n
TitleCrystal structure of class D beta-lactamase from Sebaldella termitidis ATCC 33386
ComponentsBeta-lactamase
KeywordsHYDROLASE / antibiotic resistance / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSebaldella termitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.601 Å
AuthorsMichalska, K. / Tesar, C. / Endres, M. / Joachimiak, A. / Satchell, K.J. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of class D beta-lactamase from Sebaldella termitidis ATCC 33386
Authors: Michalska, K. / Tesar, C. / Endres, M. / Joachimiak, A. / Satchell, K.J. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5144
Polymers30,2301
Non-polymers2843
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-25 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.510, 97.546, 40.328
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-658-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 30230.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sebaldella termitidis (bacteria) / Strain: ATCC 33386 / NCTC 11300 / Gene: Sterm_0301 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: D1ALR7, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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.: 274 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0. 2 M Li2SO4, ).1 M Tris/HCl, pH 8.5, 25% PEG3350, cryo 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2018 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 32985 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Net I/σ(I): 17.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.338 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 1543 / CC1/2: 0.603 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3161: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.601→27.916 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 1645 5 %
Rwork0.1598 --
obs0.1619 32929 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→27.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 16 274 2386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092208
X-RAY DIFFRACTIONf_angle_d1.0612975
X-RAY DIFFRACTIONf_dihedral_angle_d13.9691330
X-RAY DIFFRACTIONf_chiral_restr0.061304
X-RAY DIFFRACTIONf_plane_restr0.006377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6008-1.64790.29871080.25862445X-RAY DIFFRACTION93
1.6479-1.70110.3021330.23282484X-RAY DIFFRACTION95
1.7011-1.76180.23171430.21762522X-RAY DIFFRACTION95
1.7618-1.83240.27161180.19982551X-RAY DIFFRACTION96
1.8324-1.91580.21561410.18282527X-RAY DIFFRACTION96
1.9158-2.01670.20511120.16292597X-RAY DIFFRACTION97
2.0167-2.1430.17451350.14462601X-RAY DIFFRACTION98
2.143-2.30840.19751660.14612593X-RAY DIFFRACTION99
2.3084-2.54060.17971470.14062688X-RAY DIFFRACTION100
2.5406-2.90790.15731380.15392712X-RAY DIFFRACTION100
2.9079-3.66230.21171470.14252710X-RAY DIFFRACTION100
3.6623-27.92050.18781570.14712854X-RAY DIFFRACTION100
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)
10.1197-0.04790.0120.1080.10190.12150.0202-0.07830.0913-0.0231-0.02030.0137-0.1077-0.0411-0.00870.13110.01770.01040.07350.00470.106315.95132.534934.7102
20.0177-0.0670.04680.3139-0.1120.54440.03380.0064-0.0282-0.0969-0.0010.05240.06280.05410.04730.0692-0.0025-0.00550.0584-0.00160.068820.96968.474917.0219
30.1105-0.0367-0.00830.05870.02510.00560.06290.1201-0.0093-0.0369-0.07440.0934-0.0149-0.0375-0.00150.1069-0.0369-0.00740.1116-0.00640.13259.0975.872119.9824
40.105-0.0191-0.02280.02330.03440.0344-0.00620.0018-0.0057-0.00840.00670.03750.0233-0.0928-0.0060.0585-0.0179-0.00650.0850.00350.0758.504616.515223.842
50.01680.01040.01020.0970.06490.07680.1034-0.0924-0.03040.08440.0012-0.00650.1591-0.0290.03020.1343-0.0289-0.00520.09910.02280.097317.12025.32234.8412
60.06620.03880.04120.0586-0.02170.02810.03330.0216-0.045-0.0279-0.00390.036-0.01110.06510.00780.0683-0.0041-0.00410.1110.00650.079922.846821.457625.7248
70.0513-0.0106-0.02990.03370.02850.0299-0.0274-0.06370.10150.0377-0.02260.0221-0.1129-0.06350.00020.10280.0058-0.01620.0978-0.00760.089720.616626.570730.9952
80.0334-0.0084-0.03670.0740.00420.0396-0.06450.1025-0.02130.01080.0033-0.054-0.1330.177800.1267-0.0273-0.01040.11730.00810.10626.532131.206224.6082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 136 )
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 172 )
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 188 )
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 222 )
7X-RAY DIFFRACTION7chain 'A' and (resid 223 through 238 )
8X-RAY DIFFRACTION8chain 'A' and (resid 239 through 264 )

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