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- PDB-6ni0: Crystal Structure of the Beta Lactamase Class D YbxI from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 6ni0
TitleCrystal Structure of the Beta Lactamase Class D YbxI from Burkholderia thailandensis
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta lactamase class D / 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 speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, Y. / Wu, R. / Endres, R. / Babnigg, G. / Joachimiak, A. / 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) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Beta Lactamase Class D YbxI from Burkholderia thailandensis
Authors: Kim, Y. / Wu, R. / Endres, R. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)28,3176
Polymers27,8971
Non-polymers4205
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-63 kcal/mol
Surface area11500 Å2
2
A: Beta-lactamase
hetero molecules

A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,63312
Polymers55,7942
Non-polymers83910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3330 Å2
ΔGint-138 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.204, 43.204, 256.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

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Components

#1: Protein Beta-lactamase


Mass: 27896.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: A8H35_26135, A8H36_11295 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z4T9G7, beta-lactamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 0.1 M MES pH 6.5, 10 % dioxane

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 11782 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 525 / CC1/2: 0.556 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4gn2

4gn2


Resolution: 2.3→42.606 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.44
RfactorNum. reflection% reflection
Rfree0.2475 580 4.97 %
Rwork0.2109 --
obs0.2128 11673 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 21 43 1993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022005
X-RAY DIFFRACTIONf_angle_d0.4842728
X-RAY DIFFRACTIONf_dihedral_angle_d23.991722
X-RAY DIFFRACTIONf_chiral_restr0.038290
X-RAY DIFFRACTIONf_plane_restr0.004350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2968-2.52790.33621480.26152591X-RAY DIFFRACTION96
2.5279-2.89360.28331290.24742742X-RAY DIFFRACTION100
2.8936-3.64540.27721470.21352773X-RAY DIFFRACTION100
3.6454-42.6130.19681560.18512987X-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)
14.3555-0.46590.85254.03960.59632.60250.21750.04890.09310.021-0.3644-0.26740.29630.61550.14570.2896-0.0061-0.00820.3279-0.02780.2099-4.047212.681188.6922
21.88191.5623-0.0961.71380.78231.65010.05790.0135-0.3439-0.10720.0230.02070.42190.37180.02260.15670.00370.03550.1961-0.0160.1681-14.53276.727779.2039
31.86320.3707-1.1450.9264-0.60661.5136-0.00560.21490.6659-0.35140.36270.6480.0917-0.6803-0.19110.2707-0.0542-0.10550.39030.06830.4247-33.195713.33172.4043
41.99570.12430.21462.2108-0.83071.3089-0.1984-0.0809-0.0696-0.36620.1420.4932-0.0713-0.27310.12060.2502-0.0502-0.06140.29970.02170.3311-32.32257.369879.157
52.1145-0.29170.08931.5246-0.24341.2901-0.19610.1935-0.1831-0.63230.0537-0.10290.22480.01830.15660.4048-0.02810.01540.2466-0.02640.1988-15.05566.623372.4822
61.98880.669-0.86241.20321.09734.07710.1741-0.12830.54330.34950.01660.0055-0.4538-0.243-0.16960.3356-0.02550.01770.1874-0.03560.3122-21.507522.237482.1497
70.3779-1.2516-0.51335.13040.68710.6901-0.11140.0108-0.1773-0.4897-0.0770.15640.06090.01730.1790.30090.03860.08950.24160.03270.3681-18.28720.443585.8669
83.18330.7586-0.59462.4129-0.24572.36850.0582-0.4468-0.24870.3592-0.33170.11230.07670.26350.23020.2628-0.00640.03760.23290.00730.2443-15.03937.379391.3596
96.37010.20831.95812.56662.07565.45310.0343-0.12050.12580.75530.00690.07870.53750.1046-0.00760.2859-0.00410.02630.23370.00290.2587-11.721515.541798.5172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 175 )
6X-RAY DIFFRACTION6chain 'A' and (resid 176 through 195 )
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 215 )
8X-RAY DIFFRACTION8chain 'A' and (resid 216 through 255 )
9X-RAY DIFFRACTION9chain 'A' and (resid 256 through 268 )

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