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- PDB-7l52: Crystal Structure of the Metallo Beta Lactamase L1 from Stenotrop... -

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Basic information

Entry
Database: PDB / ID: 7l52
TitleCrystal Structure of the Metallo Beta Lactamase L1 from Stenotrophomonas maltophilia Determined by Serial Crystallography
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / metallo beta lactamase / serial crystallography / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


beta-lactam 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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWilamowski, M. / Kim, Y. / Sherrell, D.A. / Lavens, A. / Maltseva, N. / Endres, M. / 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 Metallo Beta Lactamase L1 from Stenotrophomonas maltophilia Determined by Serial Crystallography
Authors: Wilamowski, M. / Kim, Y. / Sherrell, D.A. / Lavens, A. / Maltseva, N. / Endres, M. / Babnigg, G. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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)29,3753
Polymers29,2441
Non-polymers1312
Water3,189177
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)117,49912
Polymers116,9764
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_445-y-1,-x-1,-z+1/31
Buried area9910 Å2
ΔGint-363 kcal/mol
Surface area38760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.668, 105.668, 99.332
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-412-

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 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: B2FTM1, beta-lactamase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7203

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 289 K / Method: batch mode
Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate ...Details: Batch crystallization done in polypropylene tubes. 200 ul of the L1 (48 mg/ml) in a buffer 0.015 Tris, 0.1 M KCl, 1.5 mM TCEP, 5 mM ZnCl2 pH 7.0 was added to 200 ul of 0.15 M sodium malonate pH 8.0, 20% (w/v) PEG3350.

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.85→46.66 Å / Num. obs: 28773 / % possible obs: 99.99 % / Redundancy: 57.37 % / Biso Wilson estimate: 6.93 Å2 / CC1/2: 0.942 / R split: 0.197 / Net I/σ(I): 4.08
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 29.22 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 1398 / CC1/2: 0.818 / R split: 0.362 / % possible all: 100
Serial crystallography sample deliveryDescription: Nylon Mesh / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: 60um Nylon mesh / Motion control: PMAC EPICS / Sample holding: ALEX mesh-holder / Support base: SmarAct XYZ stage
Serial crystallography data reductionFrames indexed: 7186 / Frames total: 38500

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
REFMAC5.8.0258refinement
MOLREPphasing
cctbx.primePRIMEdata scaling
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6UA1

6ua1


Resolution: 1.85→46.65 Å / SU ML: 0.1717 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 17.3787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2167 1441 5.06 %
Rwork0.1752 27055 -
obs0.1773 28496 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.42 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 0 177 2165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572050
X-RAY DIFFRACTIONf_angle_d0.76142804
X-RAY DIFFRACTIONf_chiral_restr0.05314
X-RAY DIFFRACTIONf_plane_restr0.0051370
X-RAY DIFFRACTIONf_dihedral_angle_d17.0366731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.25991480.22652645X-RAY DIFFRACTION100
1.92-1.990.24551310.20962660X-RAY DIFFRACTION99.96
1.99-2.080.22361340.19742664X-RAY DIFFRACTION100
2.08-2.190.24441580.18282634X-RAY DIFFRACTION100
2.19-2.330.23211450.1812659X-RAY DIFFRACTION99.96
2.33-2.510.22411480.18262686X-RAY DIFFRACTION100
2.51-2.760.23161300.18272704X-RAY DIFFRACTION100
2.76-3.160.22531340.17352733X-RAY DIFFRACTION100
3.16-3.980.17361470.14492754X-RAY DIFFRACTION99.97
3.99-46.650.1881660.14422916X-RAY DIFFRACTION99.97
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)
14.25064290847-1.611313906712.782772200240.686633124664-0.9036119598332.14046914077-0.03659387112750.2193119264030.09626571788550.0904671778538-0.0918879223475-0.230910716452-0.09501277136320.2585452650540.1190883524940.1400597792780.034040390981-0.04764031361370.1337038140170.0220845495810.173472909464-25.9574273001-19.77991726587.63693000315
21.02046189023-0.2725307402090.0436116575520.894438403424-0.007763733861210.544568971621-0.0628127675168-0.074637259570.09558066652360.06521169329280.01524040720420.128600621551-0.0951400644724-0.109320909208-0.01540107286730.04461485885940.0522823484699-0.02700512181510.0626985913304-0.01292869222150.0656896061027-36.2828832847-24.91176030349.08133724098
30.15417566544-0.07300857059710.03153775126140.2042056844660.03378132437360.192313877968-0.0308155900492-0.008104213993610.01614076683080.00812680346605-0.04831838018070.0182679840969-0.0278908697663-0.0142009751519-0.0763238596286-0.006915991981750.0794802535785-0.03488651864820.0364657586170.007738616663270.0331674421116-29.8899332998-36.52213355136.08328186433
41.8145024338-0.06917007312450.055305329961.1369587114-0.4852100304960.8819250183310.01465604420280.09388290999670.231051129749-0.07385766641890.01975843303750.220972129002-0.14553362838-0.181392926743-0.08054864217240.1010130787910.12297666739-0.06022528582660.102274719517-0.01682576915520.109222454147-42.9325500086-27.0082036162-6.06105570005
51.71812541282-1.498077661420.3615364725852.45058326034-0.6267980341390.3885888608570.03855254000250.0259670999818-0.0450348388132-0.128624169139-0.123831065065-0.1795397746130.1057303430220.1673998690220.09267531140040.0840542611850.0451229144540.0286468653040.1134407492270.06945650011360.0752363127451-15.6062055208-36.0926063341-5.24489423229
64.41449141672-1.341562285591.530280524390.705891961312-0.5868541119461.348542901110.1050988557160.0239872407294-0.156874052798-0.135133115276-0.06104845937130.04221008702660.0859312211963-0.00154566677972-0.06912126565560.1205979939560.0730476144530.01151549035620.08716012530030.02571564636810.0432795723862-24.0927836979-36.4607223685-12.6674136804
70.861376548725-0.0741899194470.3472713773760.587778390306-0.1421892371170.767372245727-0.02723522335550.06391128718490.184648542130.004502799018750.02656473924280.0933167757878-0.155960357193-0.08607008643980.003192106414520.1530229846770.0708527100449-0.05188161824620.06986150873080.04088483275770.10269940508-33.8919961074-18.5943004299-7.2032208999
83.61734916231-1.675224375140.7791055496582.43169955352-1.471117592922.40308650201-0.006625280794560.2959534200940.257160123908-0.21434197271-0.189476906587-0.3214470644980.1668743908220.3282918569190.2108260552790.1908098010660.06190045323610.02823740352020.1396453839960.0968514447580.129290854177-17.8729943838-28.3677564165-14.5829131377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 204 )
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 222 )
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 236 )
7X-RAY DIFFRACTION7chain 'A' and (resid 237 through 266 )
8X-RAY DIFFRACTION8chain 'A' and (resid 267 through 287 )

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