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- PDB-6u2z: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrop... -

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Basic information

Entry
Database: PDB / ID: 6u2z
TitleCrystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the complex with the hydrolyzed moxalactam and two copper ions
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / lactam antibiotics / moxalactam / 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; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3P7 / COPPER (II) ION / beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 complex with the hydrolyzed moxalactam and two copper ions
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 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 ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7685
Polymers29,1731
Non-polymers5964
Water1,09961
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)119,07320
Polymers116,6914
Non-polymers2,38216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area9980 Å2
ΔGint-38 kcal/mol
Surface area38510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.234, 104.234, 98.793
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: 29172.857 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 (E. coli) / Strain (production host): BL21DE3 / Variant (production host): gold / References: UniProt: B2FTM1, beta-lactamase
#2: Chemical ChemComp-3P7 / (2R)-2-[(1R)-1-{[(2R)-2-carboxy-2-(4-hydroxyphenyl)acetyl]amino}-1-methoxy-2-oxoethyl]-5-methylidene-5,6-dihydro-2H-1,3 -oxazine-4-carboxylic acid / MOXALACTAM DERIVATIVE (open form)


Mass: 406.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N2O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 13193 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 35.72 Å2 / Rmerge(I) obs: 0.181 / Net I/σ(I): 11.93
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 638 / CC1/2: 0.837 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6U0Y

6u0y


Resolution: 2.38→43.34 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.24
RfactorNum. reflection% reflection
Rfree0.2292 648 4.92 %
Rwork0.1857 --
obs0.1877 13167 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.5 Å2
Refinement stepCycle: LAST / Resolution: 2.38→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 35 61 2091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022091
X-RAY DIFFRACTIONf_angle_d0.5512858
X-RAY DIFFRACTIONf_chiral_restr0.041317
X-RAY DIFFRACTIONf_plane_restr0.004377
X-RAY DIFFRACTIONf_dihedral_angle_d14.6511241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.560.25641230.22682418X-RAY DIFFRACTION99
2.56-2.820.28951270.22672468X-RAY DIFFRACTION100
2.82-3.230.25751310.21552458X-RAY DIFFRACTION100
3.23-4.070.21741160.18462530X-RAY DIFFRACTION100
4.07-43.340.20051510.15232645X-RAY DIFFRACTION99
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)
10.9768000245-0.3226000071-0.58139997720.73659998180.3425999880.94800001380.00609999990.2246000022-0.4207000136-0.1916999966-0.14429999890.02789999920.0847000033-0.02180000020.14810000360.33120000360.02840000020.01090000010.26850000020.02360000090.323500007424.707399368319.32530021677.8084998131
20.8319000006-0.5264000297-0.32049998641.37070000170.26669999960.8869000077-0.1128999963-0.10980000350.01460000030.19480000440.0223999992-0.06819999960.08990000190.04919999840.07959999890.31220000980.02610000040.01209999990.30550000070.01040.271800011435.458599090625.96229934699.9898004532
31.12230002880.15700000520.04699999841.3668999672-0.35220000150.82220000030.00749999980.10920000080.01779999960.115699999-0.0711999983-0.0502000004-0.0502000004-0.02260000070.08039999750.25760000940.0044-0.01119999960.2509999871-0.02639999990.264999985731.975400924733.98419952390.9724000096
41.6001000404-0.1753000021-0.48930001261.09430003170.0794000031.1550999880.0623000003-0.04089999940.1758999974-0.13179999590.00949999970.01899999940.1460999995-0.0227000006-0.06289999930.2917000055-0.0015-0.04360000040.3208999932-0.03330000120.315800011218.378299713136.4047012329-8.5493001938
51.5156999826-0.26699998970.22239999472.2044999599-0.14219999311.45179998870.17779999970.3465999961-0.0722000003-0.06150000170.1313000023-0.08250000330.1782999933-0.1110000014-0.37000000480.2876999974-0.0055999998-0.01480.3095999956-0.00949999970.327199995533.003700256324.4722995758-7.7871999741
61.68640005590.0077999998-0.34769999981.4752999544-0.00689999992.10489988330.04230000080.0439000018-0.3989999890.0669-0.1177999973-0.22650000450.736899972-0.13070000710.08120000360.3490000069-0.03209999950.03799999880.260800004-0.0657000020.41589999233.10950088514.0437002182-7.1592998505
73.0316998959-1.0580999851-0.61089998481.0800000429-0.14550000430.54269999270.40020000930.3592999876-0.1626999974-0.2845999897-0.23610000310.03629999980.4393999875-0.1357000023-0.15080000460.5034000278-0.0089999996-0.03379999850.4295000136-0.05050000180.400999993116.92350006127.9659996033-14.4084997177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 204 )
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 235 )
5X-RAY DIFFRACTION5chain 'A' and (resid 236 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 266 )
7X-RAY DIFFRACTION7chain 'A' and (resid 267 through 288 )

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