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- PDB-6uaf: Crystal Structure of the Metallo-beta-lactamase L1 from Stenotrop... -

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Basic information

Entry
Database: PDB / ID: 6uaf
TitleCrystal Structure of the Metallo-beta-lactamase L1 from Stenotrophomonas maltophilia in the Complex with Hydrolyzed Imipnem
ComponentsPutative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)
KeywordsHYDROLASE / lactam antibiotics / carbapenem / 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
Chem-HIW / beta-lactamase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 Hydrolyzed Imipnem
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 ...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 1.3Oct 30, 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)31,6174
Polymers31,1691
Non-polymers4483
Water3,999222
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)126,47016
Polymers124,6774
Non-polymers1,79312
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 area9090 Å2
ΔGint-45 kcal/mol
Surface area39040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.835, 104.835, 98.627
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-442-

HOH

21A-609-

HOH

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Components

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


Mass: 31169.312 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) / Variant (production host): gold / References: UniProt: B2FTM1, beta-lactamase
#2: Chemical ChemComp-HIW / (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid / Hydrolyzed Imipenem


Mass: 317.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
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-BM / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26020 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 23.94 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Net I/σ(I): 40.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 6.29 / Num. unique obs: 1258 / CC1/2: 0.966 / % possible all: 100

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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: 1.9→34.31 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.36
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 1265 5.02 %random
Rwork0.172 ---
obs0.1738 25212 96.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 23 222 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062090
X-RAY DIFFRACTIONf_angle_d0.782856
X-RAY DIFFRACTIONf_chiral_restr0.049320
X-RAY DIFFRACTIONf_plane_restr0.006376
X-RAY DIFFRACTIONf_dihedral_angle_d10.371673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.25491250.21282644X-RAY DIFFRACTION98
1.97-2.060.2521220.20012647X-RAY DIFFRACTION98
2.06-2.170.24651270.19422623X-RAY DIFFRACTION97
2.17-2.30.23851520.18942610X-RAY DIFFRACTION97
2.3-2.480.24511600.19722547X-RAY DIFFRACTION95
2.48-2.730.27761380.20612604X-RAY DIFFRACTION96
2.73-3.130.24651380.20222640X-RAY DIFFRACTION96
3.13-3.940.17671520.15372708X-RAY DIFFRACTION97
3.94-34.310.14651510.13312924X-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)
10.3562-0.2126-0.5780.58020.43141.23-0.01180.0925-0.26960-0.11480.04850.0993-0.04320.09720.2640.0368-0.00230.22370.01660.251224.441719.86267.993
21.2412-0.4798-0.32911.2787-0.26741.1934-0.0437-0.0949-0.04960.0452-0.009-0.16250.05840.11810.050.15820.0413-0.00190.17610.00350.159235.723926.27269.9826
30.6329-0.01930.08010.9551-0.28590.608-0.0318-0.0512-0.0110.0628-0.0407-0.0552-0.02530.04080.07760.1850.0505-0.00110.204-0.00060.189728.341937.15073.7415
41.84740.3041-0.19631.42880.17541.84120.03210.3708-0.3876-0.3003-0.1982-0.35570.24270.21290.08940.22710.08290.07470.30770.02730.325942.481326.6676-6.3703
51.8016-0.08050.16151.4411-0.08041.17370.05360.08210.0295-0.2619-0.05320.13830.0137-0.026-0.01670.23730.0557-0.02980.2126-0.01440.187822.178534.5996-8.8088
61.5024-0.1353-0.68851.0618-0.06982.1103-0.06290.113-0.465-0.03090.0402-0.03690.4486-0.00530.08690.35060.06850.01990.2083-0.02550.260332.159315.8157-6.308
74.1215-1.73331.26232.0591-0.25951.320.26990.0952-0.1045-0.2927-0.10.18020.2906-0.1587-0.17170.33180.0412-0.05260.2806-0.04980.233616.603628.1036-14.1269
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 185 )
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 204 )
5X-RAY DIFFRACTION5chain 'A' and (resid 205 through 244 )
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 266 )
7X-RAY DIFFRACTION7chain 'A' and (resid 267 through 289 )

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