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- PDB-6t5l: MYO-1 from Myroides odoratimimus. Environmental metallo-beta-lact... -

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Basic information

Entry
Database: PDB / ID: 6t5l
TitleMYO-1 from Myroides odoratimimus. Environmental metallo-beta-lactamases exhibit high enzymatic activity under zinc deprivation
ComponentsSubclass B1 metallo-beta-lactamase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / carbapenemase / environmental / metallo-beta-lactamase / MBL
Function / homologyMetallo-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 / Subclass B1 metallo-beta-lactamase
Function and homology information
Biological speciesMyroides odoratimimus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsFrohlich, C.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2013-08633 Sweden
Swedish Research Council2018-02835 Sweden
CitationJournal: J.Antimicrob.Chemother. / Year: 2020
Title: Structural and biochemical characterization of the environmental MBLs MYO-1, ECV-1 and SHD-1.
Authors: Frohlich, C. / Sorum, V. / Huber, S. / Samuelsen, O. / Berglund, F. / Kristiansson, E. / Kotsakis, S.D. / Marathe, N.P. / Larsson, D.G.J. / Leiros, H.S.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 2, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Subclass B1 metallo-beta-lactamase
B: Subclass B1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9227
Polymers53,6362
Non-polymers2865
Water2,558142
1
A: Subclass B1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9734
Polymers26,8181
Non-polymers1553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Subclass B1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9493
Polymers26,8181
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.684, 144.684, 53.306
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Subclass B1 metallo-beta-lactamase


Mass: 26818.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myroides odoratimimus (bacteria) / Gene: AS202_20055 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U3H0V9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 32-36% PEG4000, 0.2 ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.17→25 Å / Num. obs: 33621 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 48.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.039 / Net I/σ(I): 11
Reflection shellResolution: 2.17→2.24 Å / Rmerge(I) obs: 0.052 / Num. unique obs: 2941 / CC1/2: 0.354 / Rpim(I) all: 0.754 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1znb

1znb


Resolution: 2.17→24.53 Å / SU ML: 0.2986 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0814
RfactorNum. reflection% reflection
Rfree0.2526 1655 4.93 %
Rwork0.2172 --
obs0.219 33586 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.83 Å2
Refinement stepCycle: LAST / Resolution: 2.17→24.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 5 142 3582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01373533
X-RAY DIFFRACTIONf_angle_d1.30124791
X-RAY DIFFRACTIONf_chiral_restr0.0714538
X-RAY DIFFRACTIONf_plane_restr0.0092619
X-RAY DIFFRACTIONf_dihedral_angle_d3.71122881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.230.37591300.3082672X-RAY DIFFRACTION99.29
2.23-2.310.3061560.2952632X-RAY DIFFRACTION99.25
2.31-2.390.27841220.24862657X-RAY DIFFRACTION99.43
2.39-2.480.30111210.23662688X-RAY DIFFRACTION99.47
2.48-2.60.26481340.22932651X-RAY DIFFRACTION99.29
2.6-2.730.29791450.21942635X-RAY DIFFRACTION98.79
2.73-2.90.26991320.2262581X-RAY DIFFRACTION95.63
2.9-3.130.2551520.21612636X-RAY DIFFRACTION98.38
3.13-3.440.26511040.20712706X-RAY DIFFRACTION99.86
3.44-3.940.23171450.18082687X-RAY DIFFRACTION99.65
3.94-4.960.19821470.17922706X-RAY DIFFRACTION99.51
4.96-24.530.27211670.25612680X-RAY DIFFRACTION96.94
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)
14.42909864625-2.94576676524-3.146374437393.666150094372.378536644662.26848648031-0.5361363528980.404671071512-0.186314526897-0.09696027674950.2924111621080.688814478396-0.142747307442-1.069729623260.2218954654610.4521491095210.143176732847-0.1295207287441.308339876230.3346864572891.298128680668.9707816213-41.8098736109-20.0693746184
28.77605800657-0.2346508258774.936432035974.06592681476-2.505610975569.42653166787-0.233900247187-0.2534891604390.82895973340.549317221438-0.1098801854670.252174581059-0.833891988431-0.1558232109550.4286907199430.4971212974810.0002632830825220.05387383016550.262330113834-0.04490580598890.43827251704755.8201704856-32.764133086-10.2331568841
32.08390509479-0.8482256833924.323352484555.6559832193-0.4101795586813.962976140140.4149341283820.915546180030.663099969224-0.695067435012-0.4809306475170.5890066667540.08158763037330.0860921889674-0.1559163955350.4437746233560.00039155013090.02791771768770.5595712182240.04078129555560.42603771812448.0177022301-38.0610332707-15.8060179299
45.535072704781.66883917234-0.1442954025123.48662508139-0.405229795492.75561371155-0.07966489430110.2236837097370.118950212592-0.05818884151070.04759149810120.0750331780863-0.326170993165-0.0184111384165-0.011451521690.377382617024-0.002693750634920.01666910545350.318851813821-0.03560666803750.25095338520458.7984232218-41.7460762839-16.7379924628
58.517887781363.75926010124-3.435191070236.33558754634-4.289478879742.11581799086-0.636236329950.808574952498-0.575450157899-0.6435254602030.5051814714170.130339095730.673762867812-0.5380955188280.08562191142790.502874127457-0.0792664757470.06552655153930.461539095081-0.09819182597850.35176683372355.3195103624-52.8452750283-21.0271865112
65.861711986152.98326570198-0.6342879412399.115824855221.553831191842.04258484889-0.1207486406730.451560761356-0.619344014702-0.3757641316080.124291296690.1135629663370.491272452359-0.4126608979690.009156605469950.346254881757-0.02035975853810.07549919180750.448398031625-0.06296654044130.37940967874258.6199207856-56.1876798776-16.1517185096
77.426158038382.75969579052-2.431440904775.37653262425-0.2569294615861.485172277230.243227447228-0.651406855835-0.9246001938070.238794021692-0.242768747404-0.0783366926770.54233389061-0.2501662370270.0163109330040.436108853997-0.03357281271570.04447280989570.333761013899-0.01252341408380.25904548115352.5867877274-53.6379131164-6.4627531907
88.641318846722.180895552522.221980136013.64709512210.9438132057574.341092291210.100007545602-0.5331495492080.2748937207540.44665348393-0.3632616404260.4361593364670.346779634173-0.509048676980.2275404884270.391308485087-0.09826956772520.103997125260.311693658078-0.0307043815740.27103347249445.487782322-47.180460585-4.66804986234
99.753260993652.210654498480.8795388713826.86723975071-3.267331012347.991411945440.305600533377-0.8389790960830.3384884645770.788933300687-0.351158978305-0.0251306403936-0.195195762463-0.1148995046030.06752783789450.411524078008-0.05666007878310.107390824590.45340728139-0.09271866935350.29640777139547.7644925797-46.72326611811.05286179807
102.01648718498-0.4963990571823.140486257868.220898321653.07201126724.728353614860.426896101341-2.008716708610.347553600521.30784373504-0.5039521118761.095438195870.763988567933-1.058442796580.2168158926350.558337112178-0.1115400959780.157102845510.6741640318-0.05845671172410.4406292304439.220215776-46.04840764692.18021949459
111.40308459315-0.733765390105-0.3838508385881.835066138650.3182197923820.1098756909290.04227105834510.4399735293840.0448506702769-0.4519305529440.400843797808-0.0884916753703-0.178278138730.434766100247-0.414332234131-0.3746752742480.500255158974-0.2751942845281.115941936350.3064088212251.228061098811.70153662921-42.7531916014-25.1086683985
120.9561193304451.27226899248-0.2391192816351.80440462221-0.923018555163.418429502960.7253971656321.069356805280.586668751651-0.212510158673-0.1840703978690.889638556997-0.397400172645-0.92606442278-0.5115594021350.5014700782120.201175109663-0.007451561887540.7795964096660.1702622544441.3837773017214.9992592521-36.3479293009-20.7681153603
135.6682923119-2.754750299623.233873658243.88118379555-3.023921546512.695021263210.1554763989071.42059719790.970354430221-0.1035565149630.7617953639610.616254515722-0.351513021357-1.21803859936-0.936200683930.8415280021040.181059784323-0.2154519048351.295226796350.4270576634631.5400675180711.9772630524-36.8690971464-29.2714240031
148.69809252051-4.016341487652.835809989839.49558405124-1.864860890112.958652192220.08480831084761.874676987060.815909214016-1.662704768450.08213114524390.866911761817-0.056319165618-0.54554117972-0.4289960890830.775632680848-0.167283946353-0.1984087798651.173763886650.3738769815190.77955565870423.980960131-44.0559014947-32.306918956
154.436267011081.250160615140.9197060238158.798266896971.160501552264.10692566258-0.3347817848410.3407125378770.892488642014-0.216580435932-0.05754382112840.949506627582-0.47180919541-0.5308450791720.3757762411910.358534711746-0.0225817661272-0.07935246394190.5628933398140.0004621275937990.57613993529724.2571805802-47.3020869702-20.7786534902
164.888874464270.7191396548630.8689120900336.853757478670.8931020084254.38243637530.100352001716-0.6962818342730.5189306885680.794999994186-0.4196020594841.248544816610.12326771106-1.002650899820.2293981334820.41243054746-0.1681765854940.1446842897070.885718537425-0.1344623107960.63160620953519.5611813477-54.0304906569-11.4825001216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 47 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 149 )
6X-RAY DIFFRACTION6chain 'A' and (resid 150 through 182 )
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 201 )
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 241 )
9X-RAY DIFFRACTION9chain 'A' and (resid 242 through 280 )
10X-RAY DIFFRACTION10chain 'A' and (resid 281 through 291 )
11X-RAY DIFFRACTION11chain 'B' and (resid 35 through 45 )
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 83 )
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 113 )
14X-RAY DIFFRACTION14chain 'B' and (resid 114 through 149 )
15X-RAY DIFFRACTION15chain 'B' and (resid 150 through 241 )
16X-RAY DIFFRACTION16chain 'B' and (resid 242 through 291 )

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