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- PDB-7uhs: SSX Structure of Metallo Beta-Lactamase L1 with Two Water Molecul... -

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Entry
Database: PDB / ID: 7uhs
TitleSSX Structure of Metallo Beta-Lactamase L1 with Two Water Molecules in the Active Site
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / metallo beta lactamase / moxalactam / serial crystallography / 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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Biological speciesStenotrophomonas maltophilia K279a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWilamowski, M. / Kim, Y. / Sherrell, D.A. / Lavens, A. / Henning, R. / Maltseva, N. / Endres, M. / Babnigg, G. / Srajer, V. / 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: Nat Commun / Year: 2022
Title: Time-resolved beta-lactam cleavage by L1 metallo-beta-lactamase.
Authors: Wilamowski, M. / Sherrell, D.A. / Kim, Y. / Lavens, A. / Henning, R.W. / Lazarski, K. / Shigemoto, A. / Endres, M. / Maltseva, N. / Babnigg, G. / Burdette, S.C. / Srajer, V. / Joachimiak, A.
History
DepositionMar 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,2441
Polymers29,2441
Non-polymers00
Water63135
1
A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)

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

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

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


Theoretical massNumber of molelcules
Total (without water)116,9764
Polymers116,9764
Non-polymers00
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 area8790 Å2
ΔGint-47 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.951, 105.951, 99.886
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

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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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
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: 295 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: 2.2→46.8 Å / Num. obs: 17385 / % possible obs: 100 % / Redundancy: 76.5 % / Biso Wilson estimate: 34.26 Å2 / CC1/2: 0.95 / R split: 0.25 / Net I/σ(I): 2.51
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 865 / CC1/2: 0.41 / % possible all: 100
Serial crystallography sample deliveryDescription: Nylon Mesh / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: ALEX mesh holder
Motion control: SmarAct Motors viaPMAC start/stop raster over area
Sample holding: nylon mesh / Support base: xyz stage
Serial crystallography data reductionCrystal hits: 5191 / Frames indexed: 4550 / Frames total: 38500 / Lattices indexed: 4550

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOLREPphasing
cctbx.primedata scaling
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L52

7l52


Resolution: 2.2→46.8 Å / SU ML: 0.3157 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 823 4.77 %
Rwork0.2214 16432 -
obs0.2231 17255 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 0 35 2016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152031
X-RAY DIFFRACTIONf_angle_d0.42982774
X-RAY DIFFRACTIONf_chiral_restr0.0383311
X-RAY DIFFRACTIONf_plane_restr0.0034364
X-RAY DIFFRACTIONf_dihedral_angle_d15.762724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.34121370.32352589X-RAY DIFFRACTION96.56
2.34-2.520.33451340.31862703X-RAY DIFFRACTION100
2.52-2.770.31241210.29142713X-RAY DIFFRACTION100
2.77-3.170.3461340.24672729X-RAY DIFFRACTION100
3.17-40.25381370.19132769X-RAY DIFFRACTION100
4-46.80.18441600.1682929X-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)
14.10129894284-2.362696351381.811712252741.4147053693-1.401046995572.94594338621-0.181338116263-0.4678059006720.8114403904780.124291870791-0.15999893833-0.864836572411-0.4008861513170.3900800205820.3362312607130.5108394503120.0920484104022-0.1238665354970.545521308210.04106393610470.777006688422-24.498861916-19.49408739318.21446392557
22.26932936621-1.082973102360.500982065422.57179935361-0.4194093943312.68356384304-0.0915375540257-0.08935503996620.06977322174850.1499931930340.1094428546380.0538941140224-0.294750166569-0.0264304403510.04365065424330.2838009239340.07369666777010.001807989104440.244823055277-0.02103702534130.260528763958-37.6932856983-24.37282722728.80447771918
31.0219568140.281249049879-0.2475086710171.841675991620.130686613542.33820898135-0.1500199855010.01822473086060.02536593403240.0123107689349-0.0881080323795-0.0149544594097-0.08475751997380.08742995432850.09949668132690.2229576632020.0496375237062-0.0277506626680.2131531552350.01436992639260.215693582297-30.2581571183-35.94667265057.3237851699
43.59822442287-0.164871851635-0.4295860129892.15135716820.08139286377132.572948146040.0712545156480.7155684148640.394901759206-0.142450217863-0.2694507740360.0870466569955-0.0959348762274-0.1377702290710.05752202705950.3105541643370.0657256997376-0.01727862707190.296466200333-0.01875885054740.288662854511-38.13213263-29.2903739068-5.26693388465
54.23975902261-2.35434440639-0.2075997664953.44698064263-0.7488172045621.839280347870.00328386857399-0.02982309514790.301510700735-0.0540335513235-0.206345112237-0.384091071178-0.173188290539-0.03349290848260.1848823420140.3212805963560.0480795677962-0.01208095635490.3937983620350.09489138366450.412402916402-15.2466891199-36.4574917154-5.47615878868
67.44512341569-2.079704592461.170695620922.88480588160.2480080629892.788395252570.08692981846260.561645606934-0.345704596968-1.04362916879-0.432911217647-0.09827962422260.3215891792550.07799652048330.07815305465570.4752821074310.115906731150.1048043576390.3641400661740.02746624976080.24572228398-24.193492452-36.6801211896-12.7650895672
72.67481058222-0.807109131119-0.10629882683.2957594370.160118058672.668183456730.005215225923760.5255921944990.375067624518-0.377060574333-0.0532854722996-0.19287676171-0.8667645813950.08075364800960.100072582870.3806163373690.0330228434409-0.01365837020240.2897563419920.0822236956750.315547895965-33.8669940698-18.8821680344-7.29736559531
88.68639202538-2.80172604283-0.1324987392384.14788173022-0.1641226287993.5225839590.3277079572250.130869831674-0.128911067118-0.385899416955-0.372115934611-0.449542928803-0.3886579314730.4460527083950.140773394040.5023161335090.0152350294840.05575272487270.3772823059620.1892937269010.455147638791-17.7430054552-28.6423305618-14.9651911456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 177 )
4X-RAY DIFFRACTION4chain 'A' and (resid 178 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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