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- PDB-6tww: Variant W229D/F290W-19 of the last common ancestor of Gram-negati... -

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Basic information

Entry
Database: PDB / ID: 6tww
TitleVariant W229D/F290W-19 of the last common ancestor of Gram-negative bacteria beta-lactamase class A (GNCA4)
ComponentsBeta-Lactamase (GNCA4)
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE / ANCESTRAL RECONSTRUCTED
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / FORMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsGavira, J.A. / Risso, V. / Sanchez-Ruiz, J.M. / Romero-Rivera, A. / Kamerlin, S.C.L.
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: Chem Sci / Year: 2020
Title: Enhancing ade novoenzyme activity by computationally-focused ultra-low-throughput screening.
Authors: Risso, V.A. / Romero-Rivera, A. / Gutierrez-Rus, L.I. / Ortega-Munoz, M. / Santoyo-Gonzalez, F. / Gavira, J.A. / Sanchez-Ruiz, J.M. / Kamerlin, S.C.L.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Jan 24, 2024Group: 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
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: Beta-Lactamase (GNCA4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,34311
Polymers28,8681
Non-polymers47510
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-18 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.230, 78.230, 198.322
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
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,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-1799-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-Lactamase (GNCA4)


Mass: 28868.441 Da / Num. of mol.: 1 / Mutation: W229D, F290W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-24b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 376 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.9 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 4.0 M Sodium formate, 100 mM Tris HCl pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.38→47.31 Å / Num. obs: 74330 / % possible obs: 99.98 % / Redundancy: 15.3 % / Biso Wilson estimate: 15.91 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0498 / Rpim(I) all: 0.0129 / Rrim(I) all: 0.0515 / Net I/σ(I): 27.24
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.6767 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 7295 / CC1/2: 0.887 / CC star: 0.969 / Rpim(I) all: 0.2266 / Rrim(I) all: 0.7146 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Cootmodel building
EDNAdata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UHU

4uhu


Resolution: 1.38→47.31 Å / SU ML: 0.1144 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.1237
RfactorNum. reflection% reflection
Rfree0.1659 2000 2.69 %
Rwork0.1505 --
obs0.1509 74324 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.22 Å2
Refinement stepCycle: LAST / Resolution: 1.38→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 30 366 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132295
X-RAY DIFFRACTIONf_angle_d1.27423145
X-RAY DIFFRACTIONf_chiral_restr0.0964356
X-RAY DIFFRACTIONf_plane_restr0.0091427
X-RAY DIFFRACTIONf_dihedral_angle_d9.70321251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.420.21431400.20795084X-RAY DIFFRACTION100
1.42-1.450.20621410.1785064X-RAY DIFFRACTION100
1.45-1.50.17821400.16365060X-RAY DIFFRACTION100
1.5-1.550.19681400.15285094X-RAY DIFFRACTION99.96
1.55-1.60.15731410.14885103X-RAY DIFFRACTION100
1.6-1.660.14831410.14035089X-RAY DIFFRACTION100
1.66-1.740.1641420.14745118X-RAY DIFFRACTION99.98
1.74-1.830.1621400.1475102X-RAY DIFFRACTION99.96
1.83-1.950.16661430.1485127X-RAY DIFFRACTION100
1.95-2.10.17131420.14125150X-RAY DIFFRACTION100
2.1-2.310.17461440.13955196X-RAY DIFFRACTION99.98
2.31-2.640.18661440.15395222X-RAY DIFFRACTION100
2.64-3.330.181470.15815303X-RAY DIFFRACTION99.98
3.33-47.310.13671550.1475612X-RAY DIFFRACTION99.97
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)
10.845647246438-0.2832327091740.04007864643170.652119650244-0.06989625023520.309583190643-0.0245323662023-0.00279802063907-0.005044201990340.02142423022690.0388832013796-0.0820405642819-0.004626461999680.0796495728843-0.009655158942140.1270832777510.00509175111033-0.006092588872340.13926415188-0.004675643874070.114735308034-15.62749488917.8265370504-13.0875731847
21.93723789137-1.780952053961.354679185514.78503480073-2.292581621022.68843327725-0.009400724340270.0614881460801-0.202715147885-0.2162964981370.03235025430230.339880330270.0318543023227-0.100514408959-0.0008439183754430.164069002972-0.0166685820544-0.01594904179090.184899127018-0.03893139213320.2283585566-39.7130339761-0.039834636283-22.7909348822
33.15252879228-1.47079420610.08890922887933.418321678090.009399515091212.37781785376-0.0645711057723-0.149228249242-0.3565918223780.2469105405960.009651246544990.1738544013890.1783675887370.06437866760780.07464967727770.198581305001-0.007848401299010.009703748544040.156987128690.01538208517230.218445919174-31.6392631931-7.58806277631-12.1392747957
40.5469702702750.1365236583580.03437624421660.9178227595890.3515473401430.733060627814-0.00459676013228-0.00329726572077-0.04965370866090.033872469006-0.0004183854186510.03032649943150.01197668662030.00368505675268-0.0004201778907290.1340864423460.00745491645722-0.008127901686670.125499852987-0.001056127992990.13415855136-24.928289996511.0200408631-15.2475528914
52.29744926414-0.08236053724060.1761906548381.6138762415-0.1172199940722.61117281337-0.0360180905183-0.1799915094250.05383430769530.2482456802150.0327790062709-0.0463706910886-0.02697806347420.0889083439703-0.01726144809520.133299208156-0.014569090798-0.02287255699290.171049485989-0.003082305207250.115985900958-15.132008151818.6769693403-3.07316061942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 258 )
5X-RAY DIFFRACTION5chain 'A' and (resid 259 through 296 )

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