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- PDB-6ua1: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrop... -

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Basic information

Entry
Database: PDB / ID: 6ua1
TitleCrystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the no-metal bound form
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / lactam antibiotics / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / 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 metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the no-metal bound form.
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3062
Polymers29,2441
Non-polymers621
Water2,270126
1
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2248
Polymers116,9764
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area9190 Å2
ΔGint-49 kcal/mol
Surface area39920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.467, 104.467, 99.035
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

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Components

#1: Protein Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)


Mass: 29243.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: Smlt2667 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: B2FTM1, beta-lactamase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium malonate pH 7.0, 20 % w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29676 / % possible obs: 98.7 % / Redundancy: 14.6 % / Biso Wilson estimate: 35.47 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 31
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 0.67 / Num. unique obs: 1215 / CC1/2: 0.552 / % possible all: 83.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6U0Y

6u0y


Resolution: 1.8→41.15 Å / SU ML: 0.2749 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 28.7856
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1511 5.13 %random
Rwork0.191 ---
obs0.1927 29445 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.63 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 0 126 2129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552092
X-RAY DIFFRACTIONf_angle_d0.77482859
X-RAY DIFFRACTIONf_chiral_restr0.0512317
X-RAY DIFFRACTIONf_plane_restr0.0057380
X-RAY DIFFRACTIONf_dihedral_angle_d13.77071243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.39461070.39592066X-RAY DIFFRACTION81.54
1.86-1.920.43171410.34182481X-RAY DIFFRACTION97.91
1.92-20.31371310.292545X-RAY DIFFRACTION99.7
2-2.090.28441380.24562546X-RAY DIFFRACTION99.52
2.09-2.20.26661370.22462551X-RAY DIFFRACTION99.93
2.2-2.340.25221390.20672554X-RAY DIFFRACTION99.93
2.34-2.520.26011420.19892582X-RAY DIFFRACTION99.85
2.52-2.780.26631300.21552595X-RAY DIFFRACTION99.85
2.78-3.180.2351420.21742610X-RAY DIFFRACTION99.78
3.18-40.22081470.17462634X-RAY DIFFRACTION99.43
4-41.150.16061570.1472770X-RAY DIFFRACTION98.85
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)
10.08347037177030.04108771587730.01036543724970.02031530557720.025986893631-0.00602370414958-0.334815284829-0.483146395877-0.229368356303-0.006736022140260.1892786572230.2059121085910.0634166359532-0.353382244426-6.39881956638E-50.7149322947490.007108322039940.06043620110890.476234408208-0.02215623623280.62006522266924.194907062-5.593042809391.83561597195
20.285744508847-0.302875657973-0.2641117092910.2817401041190.1833727648140.362594394425-0.05588115305680.06026574250550.05473711750470.053169360749-0.02571504693150.131874100066-0.16544556874-0.230509223403-0.0001140785799250.4936122904180.0382166309775-0.04640650790080.294662905725-0.01589152926560.40293385596435.555544199821.26897431049.61941393232
30.185124355445-0.287749704395-0.1168429901770.3213491736480.05076957535850.178853532249-0.04722312203150.122300368349-0.0486375510939-0.189204394947-0.0590381924113-0.0754500435733-0.194964966274-0.04155466674320.0002702111398780.4849846380130.0237379310775-0.02502277754490.320904559472-0.01138011375710.32365590553142.989908793415.73108998914.76365680866
40.326197229249-0.424314391440.09078096250610.468909293574-0.1501974723110.2031563530950.03182592571270.0184446991241-0.08852685304640.151799002487-0.0755229650030.09733463382920.0308457012069-0.09572700114752.53571533539E-50.437029120550.04126070705130.01239806845570.31290590227-0.02645062729470.34874024516645.20401455972.671782040179.69470497432
51.00314811037-0.4790206087870.1347293905120.614085857014-0.6229946628690.637634590973-0.186067243735-0.1244394077350.06111532484970.4101497003770.0525447913154-0.0125754773149-0.02366836811610.0408335044139-0.0001369322388220.4931551949340.020370464419-0.01679246134430.250511485992-0.02920631835280.32624505713943.514404911611.785212588421.2443980526
60.3328974979280.146834354131-0.1162417391870.0808158994833-0.03362977982180.140521579891-0.0551861871069-0.2524873396090.01394998748620.68446340914-0.153771794677-0.122934793978-0.1678613562580.07001015425990.0002068784902870.5628647355180.0810349886030.00188732154650.354268491760.005297416725530.35970651801942.26455902368.0348409374928.1682247035
70.07062954681430.052072839118-0.07443334980010.0266600944319-0.05969610511020.0808764576065-0.1471078753220.04645357258420.05887925070160.4512078284040.3671590406140.180437606827-0.0429493754844-0.7434694315690.001677029839720.5390550605670.1351723032310.03566307071080.459973990816-0.02347032585150.38376481360929.607981851219.849592525422.8760402566
80.298793573638-0.3624456738520.1753864743940.434998634329-0.1491121273150.0805919515063-0.223641771465-0.04777845110850.01442339672320.2465604445670.4496502631610.453043705501-0.233676810567-0.9800749436970.04728770900990.5674052648060.0978164791010.1646823159880.530633854062-0.001102455550910.4056008321333.0527731110.97512851447831.1315329587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 222 )
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 244 )
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 266 )
8X-RAY DIFFRACTION8chain 'A' and (resid 267 through 288 )

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