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- PDB-6yrs: Structure of a new variant of GNCA ancestral beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 6yrs
TitleStructure of a new variant of GNCA ancestral beta-lactamase
Componentsancestral beta-lactamase
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / ANCESTRAL RECONSTRUCTED
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGavira, J.A. / Risso, V. / Martinez-Rodriguez, S. / Sanchez-Ruiz, J.M. / Modi, T. / Ozkan, S.B.
Funding support Spain, United States, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-74875-P Spain
Spanish Ministry of Economy and CompetitivenessBIO2015-66426-R Spain
Human Frontier Science Program (HFSP)RGP0041/2017 United States
CitationJournal: Nat Commun / Year: 2021
Title: Hinge-shift mechanism as a protein design principle for the evolution of beta-lactamases from substrate promiscuity to specificity.
Authors: Modi, T. / Risso, V.A. / Martinez-Rodriguez, S. / Gavira, J.A. / Mebrat, M.D. / Van Horn, W.D. / Sanchez-Ruiz, J.M. / Banu Ozkan, S.
History
DepositionApr 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_radiation_wavelength / diffrn_source
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: ancestral beta-lactamase
B: ancestral beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,68022
Polymers57,7502
Non-polymers1,93020
Water4,558253
1
A: ancestral beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,19414
Polymers28,8751
Non-polymers1,31913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ancestral beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4868
Polymers28,8751
Non-polymers6117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.347, 81.402, 61.037
Angle α, β, γ (deg.)90.000, 94.580, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ancestral beta-lactamase


Mass: 28874.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-24b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 6 types, 273 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.42 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 9
Details: 100 mM Tris-HCl pH 9.0, 20% PEG200, 15% PEG4K, 10% PEG8K
PH range: 5.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2018 / Details: monocromator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→48.73 Å / Num. obs: 49578 / % possible obs: 97.68 % / Redundancy: 3 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.03
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 2.9 % / Num. unique obs: 4871 / CC1/2: 0.588 / % possible all: 96.72

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B88

4b88


Resolution: 1.7→48.73 Å / SU ML: 0.206 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9045
RfactorNum. reflection% reflection
Rfree0.2084 2530 5.1 %
Rwork0.176 --
obs0.1776 49570 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.92 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 126 253 4179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124241
X-RAY DIFFRACTIONf_angle_d1.10195722
X-RAY DIFFRACTIONf_chiral_restr0.0599648
X-RAY DIFFRACTIONf_plane_restr0.0076756
X-RAY DIFFRACTIONf_dihedral_angle_d9.87223387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.35561320.32692561X-RAY DIFFRACTION97.47
1.73-1.770.27571290.29082590X-RAY DIFFRACTION95.84
1.77-1.810.30981480.27242594X-RAY DIFFRACTION97.61
1.81-1.850.27931620.252585X-RAY DIFFRACTION97.72
1.85-1.890.28811420.2322619X-RAY DIFFRACTION98.19
1.89-1.950.22831470.20632594X-RAY DIFFRACTION98.14
1.95-20.21871640.19052607X-RAY DIFFRACTION98.33
2-2.070.20941480.17772613X-RAY DIFFRACTION98.05
2.07-2.140.22971380.17372563X-RAY DIFFRACTION97.16
2.14-2.230.17921230.1662642X-RAY DIFFRACTION97.74
2.23-2.330.19511340.16822632X-RAY DIFFRACTION98.05
2.33-2.450.20891180.16422650X-RAY DIFFRACTION97.91
2.45-2.610.20511460.16092645X-RAY DIFFRACTION98.83
2.61-2.810.18271440.16462607X-RAY DIFFRACTION98.07
2.81-3.090.24041070.18052676X-RAY DIFFRACTION97.99
3.09-3.540.23261450.16362626X-RAY DIFFRACTION98.3
3.54-4.450.1661740.14912584X-RAY DIFFRACTION96.77
4.45-48.730.21271290.18482652X-RAY DIFFRACTION96.23
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)
12.932590477011.0830629206-1.2598957396.5835516675-0.9902845654351.82098032609-0.05636531167470.3000093525660.222411498023-0.1953463939270.2093064686880.966759067878-0.141840983392-0.375856355021-0.1520801851580.2547208778560.022066883797-0.02243746123420.32321249057-0.01806615445360.39720539413310.241152977546.3579503186-3.76235679859
22.85902944193-0.0737647328802-0.4015949631335.15187619044-0.2375585123481.597413559520.0544076379294-0.2283300455070.1135986417060.288333513605-0.0687747424807-0.655340351381-0.1198591194470.268004833682-0.01657148341550.28577883041-0.0425497127861-0.02521180443410.3283510365210.02465907615570.27787851078838.774501666738.566446854.76292303717
34.675493206090.794431757658-0.8011426753026.17593609099-0.6740318643692.8682053411-0.01822278188280.132285828254-0.434019861967-0.373468184318-0.0833971181788-0.5044031833320.3908787728530.2062704304840.1210895924030.3462082801070.006887767716590.01172208455230.3002051605060.01957803315760.3470146682538.02372800523.4907883181-0.442863006981
42.38417933082-0.2626059075250.4542446851232.33209579618-0.1075203831732.834164064910.0200143448136-0.3491449741480.0009118869761820.1392825924290.01789413178290.021223602094-0.100084164587-0.111160934387-0.006185302519390.260271673568-0.03533657012610.0007011049213560.2304062789380.02303434795170.20501391133428.29093940836.31773339716.75319578695
53.28248512984-1.409115089032.492499033715.15614662557-0.4992825158222.0740068013-0.0292056987449-0.007120469057370.4250442840120.2057977209790.1054773346420.0476868390476-0.157015663834-0.183449028535-0.01692901007080.2625581588220.01835248063650.02168926229540.209561280452-0.02459761474990.1961479362123.535162366349.29049457721.85992135186
63.081654144280.245245934291.582536216811.90215411432-0.3733528774944.19303383978-0.05017896598550.2270031483730.5421616171640.150392693589-0.110382962982-0.346518900546-0.3994758090850.2740030830690.3802858151720.396873557988-0.0862346816664-0.02005017594640.2737009295210.04845217610210.40173038521336.861633419149.2281614361-2.70428900522
72.82052586321-0.7709927199290.7471992056331.91578310933-1.872899997814.384868254880.001340347533880.3481148765870.0639010350291-0.459889417398-0.0742207966464-0.0538470295769-0.04014032778720.0164947883590.09391155340310.407639919094-0.01185906462570.01280633251930.291557963665-0.03549407308780.23673457659325.934048724341.9729721142-13.870194326
86.136475640454.58220828665-1.115782687728.63342590721-1.560408905552.60805221688-0.0006118189238040.08809400096790.0977206844653-0.3611415741860.09066455564220.4396002098260.0558112107283-0.0374202321536-0.05589889913860.2643191923580.0205968633228-0.02394813337970.210803419819-0.02050489667270.17971231397918.143870224441.8803897319-6.65654939743
94.810505345520.9434214500090.15306861327.218744993860.2912423426254.83701423238-0.2830690231490.3513032882410.461740386657-1.271766328590.3571381312180.32860333294-0.13556697033-0.148726628204-0.07482810612050.401526173150.0168636452973-0.1071976119590.317764383350.0028681674450.26746642003713.550890422745.499698949-13.8068821958
103.175218458231.20158818642-0.7634251721632.83159160305-0.3076926483011.384673530530.00226829409362-0.214489825905-0.1651047441860.158088381292-0.00860036042219-0.184785468714-0.08801503832340.1399937756220.004155083478710.265757152390.00977671355196-0.002362168886240.30437467714-0.0005014537399130.21289963522346.846845696832.875488320927.7126805929
115.55372542291-0.610896008331-1.801815015562.626655839070.1324950044942.5919259697-0.349477352987-0.2858814286870.2495012200060.904814849335-0.135380981878-0.590849806225-0.2636246225330.1908709409730.4802937722180.6408716184240.055571837088-0.1311838271390.4326856371620.05868941695130.41523143845442.348062875229.265057635437.1090295411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 179 )
5X-RAY DIFFRACTION5chain 'A' and (resid 180 through 195 )
6X-RAY DIFFRACTION6chain 'A' and (resid 196 through 212 )
7X-RAY DIFFRACTION7chain 'A' and (resid 213 through 238 )
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 271 )
9X-RAY DIFFRACTION9chain 'A' and (resid 272 through 294 )
10X-RAY DIFFRACTION10chain 'B' and (resid 28 through 195 )
11X-RAY DIFFRACTION11chain 'B' and (resid 196 through 293 )

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