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Basic information

Entry
Database: PDB / ID: 7luu
TitleKinetic and Structural Characterization of the First B3 Metallo-beta-Lactamase with an Active Site Glutamic Acid
ComponentsSubclass B3 metallo-beta-lactamase
KeywordsHYDROLASE / antibiotic degradation
Function / homology: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / metal ion binding / Subclass B3 metallo-beta-lactamase
Function and homology information
Biological speciesSphingobium indicum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsWilson, L. / Knaven, E. / Morris, M.T. / Schenk, G.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1084778 Australia
CitationJournal: Antimicrob.Agents Chemother. / Year: 2021
Title: Kinetic and Structural Characterization of the First B3 Metallo-beta-Lactamase with an Active-Site Glutamic Acid.
Authors: Wilson, L.A. / Knaven, E.G. / Morris, M.T. / Monteiro Pedroso, M. / Schofield, C.J. / Bruck, T.B. / Boden, M. / Waite, D.W. / Hugenholtz, P. / Guddat, L. / Schenk, G.
History
DepositionFeb 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Subclass B3 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,80427
Polymers32,4511
Non-polymers2,35326
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.640, 75.420, 56.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-682-

HOH

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Components

#1: Protein Subclass B3 metallo-beta-lactamase


Mass: 32451.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium indicum (strain DSM 16412 / CCM 7286 / MTCC 6364 / B90A) (bacteria)
Strain: DSM 16412 / CCM 7286 / MTCC 6364 / B90A / Gene: SIDU_11385 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1L5BQA7
#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: in 0.2 M LiSO4, 0.1 M Tris, pH 8.5, and 1.26 M NH4SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 16, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.68→48.19 Å / Num. obs: 31438 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 18.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Χ2: 0.54 / Net I/σ(I): 20.1
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1534 / CC1/2: 0.902 / Rpim(I) all: 0.19 / Rrim(I) all: 0.697 / Χ2: 0.47 / % possible all: 97.2

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VPE

3vpe


Resolution: 1.68→48.19 Å / SU ML: 0.1255 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.2054
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1697 2000 6.37 %
Rwork0.1414 29397 -
obs0.1433 31397 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.1 Å2
Refinement stepCycle: LAST / Resolution: 1.68→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 143 290 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01972203
X-RAY DIFFRACTIONf_angle_d1.54912950
X-RAY DIFFRACTIONf_chiral_restr0.1113301
X-RAY DIFFRACTIONf_plane_restr0.0109378
X-RAY DIFFRACTIONf_dihedral_angle_d26.2626818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.19941390.17222037X-RAY DIFFRACTION97.97
1.72-1.770.21211400.15372056X-RAY DIFFRACTION100
1.77-1.820.18111400.14862062X-RAY DIFFRACTION100
1.82-1.880.17921410.13612088X-RAY DIFFRACTION100
1.88-1.940.14971420.13232073X-RAY DIFFRACTION100
1.94-2.020.17031420.12892086X-RAY DIFFRACTION100
2.02-2.110.15571410.13612070X-RAY DIFFRACTION100
2.11-2.220.19221410.13342089X-RAY DIFFRACTION100
2.22-2.360.17711430.14272099X-RAY DIFFRACTION100
2.36-2.550.20221430.14592088X-RAY DIFFRACTION100
2.55-2.80.18191430.14692116X-RAY DIFFRACTION100
2.8-3.210.16711440.1432109X-RAY DIFFRACTION100
3.21-4.040.16291470.12772168X-RAY DIFFRACTION99.96
4.04-48.190.14811540.15162256X-RAY DIFFRACTION99.92
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)
11.58161380564-0.647916796464-0.8194441718431.973938341740.1921884599012.329222897630.04972800714090.06708074878960.20173021658-0.1239204976810.0551660139969-0.112094610561-0.1888837323130.107834016212-0.07551865540640.129464279004-0.0200618203153-0.01670657848960.144938124363-0.01127794149480.13342024823418.380070619331.171049006818.4758356598
21.53551974837-0.30576851884-0.2185279176952.06486029901-0.4224335824582.1864541624-0.0435495344727-0.1171508090140.06877605683080.1774235831250.05569746378840.0752584755922-0.06402806663120.14541955082-0.05627877383350.1441347251310.02183257683380.003242551183650.137777546803-0.004804420788810.14122624881312.511471707128.31065980325.5564557465
31.1527297599-0.28751054915-0.2850889635771.143773553560.4460311535861.58357115857-0.0593907189371-0.02867537328470.06257963665523.11435373378E-50.109954945066-0.211844757366-0.05553786829910.141442485079-0.05229380973160.1405702125140.0169168292445-0.01173762392640.137097865146-0.01117308193490.1492426366419.65622617828.236554505423.1184467913
41.00451153751-0.06321121794060.1518461066781.086318483670.4989507018420.735419944395-0.0318026124932-0.0469484684696-0.03199511391470.09588408166170.0704238282651-0.10968611791-0.008062873974760.130136378022-0.0308625859840.136068112290.0162244498722-1.30396455111E-50.1541296042490.006196762414220.15392159836717.502472795820.830959653322.9551595068
52.3599064518-0.178549833605-0.2982307144680.783759457846-0.0453493304641.57441943127-0.05171779435920.0363433445173-0.1845310070030.009534136585090.03206288140040.06215741677030.1446665275690.04285013383120.00567301431710.1716856094180.0072071346964-0.004294471039890.126150567162-0.007221336955140.19590528519911.011363720313.972905976715.9028795499
61.076161085420.1238492270070.4111605158311.151306801770.4609140792062.685386416710.01089421373650.0666691052002-0.01841578013210.03647141662950.0613173542170.0969014334095-0.0215763004530.0165918455278-0.1058093488170.116852905359-0.0006525680737430.002359666022080.1228796020420.01420587418450.174538535033.3439739953922.620628145613.5155124175
71.87827230761-1.1531846212-1.820880997612.460204267881.862949246493.78496703165-0.06004294531360.0657623653399-0.220527027327-0.115527091736-0.1856173122150.521880117419-0.0126741392789-0.2685094356460.2594041504420.179159178281-0.0299587176322-0.04448871824410.202419613049-0.004482333387050.267794765684-3.5111416218116.72118522217.30442115128
80.847684202844-0.5532108666590.1938818056620.9399206240970.3166509724990.867631740528-0.0344135904736-0.04012414052530.01208009153820.04756683960580.05909384184070.0610343903199-0.0527641382332-0.149030737084-0.0356032421020.1713162075510.02539070998420.004821405544010.1431101039680.0147823654090.1696575298661.1048861971532.193159514518.6460289763
90.5775606402070.3589983647780.3090277080531.849636019192.313389736776.01079334982-0.1422787122230.1963137318580.0543152817106-0.3924762522860.04123258079190.292802587928-0.569763513642-0.05376288667790.06918479920710.21347709172-0.0207218176053-0.0755190711860.1979290386430.03936706144730.23110532434-3.2076053730226.2452409310.182371492579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 66 )
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 125 )
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 176 )
6X-RAY DIFFRACTION6chain 'A' and (resid 177 through 218 )
7X-RAY DIFFRACTION7chain 'A' and (resid 219 through 237 )
8X-RAY DIFFRACTION8chain 'A' and (resid 238 through 261 )
9X-RAY DIFFRACTION9chain 'A' and (resid 262 through 284 )

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