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- PDB-5fqj: W229D mutant of the last common ancestor of Gram-negative bacteri... -

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Basic information

Entry
Database: PDB / ID: 5fqj
TitleW229D mutant of the last common ancestor of Gram-negative bacteria (GNCA) beta-lactamase bound to 5(6)-nitrobenzotriazole (TS-analog)
ComponentsGNCA LACTAMASE W229D
KeywordsHYDROLASE / PRECAMBRIAN / RESURRECTED BETA-LACTAMASE / GNCA
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / 6-NITROBENZOTRIAZOLE
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.271 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S. / Risso, V.A. / Sanchez-Ruiz, J.M.
CitationJournal: Nat Commun / Year: 2017
Title: De novo active sites for resurrected Precambrian enzymes.
Authors: Risso, V.A. / Martinez-Rodriguez, S. / Candel, A.M. / Kruger, D.M. / Pantoja-Uceda, D. / Ortega-Munoz, M. / Santoyo-Gonzalez, F. / Gaucher, E.A. / Kamerlin, S.C.L. / Bruix, M. / Gavira, J.A. / Sanchez-Ruiz, J.M.
History
DepositionDec 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Source and taxonomy / Structure summary
Revision 1.2Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GNCA LACTAMASE W229D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9272
Polymers28,7621
Non-polymers1641
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.172, 69.793, 69.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GNCA LACTAMASE W229D


Mass: 28762.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: beta-lactamase
#2: Chemical ChemComp-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTANT W229D HISTAG

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 9
Details: TRIS-HCL 0.1M PH9.0, PEG 400 20%, PEG 4000 15%, PEG 8000 10%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.27→41.3 Å / Num. obs: 11969 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.66
Reflection shellResolution: 2.27→2.36 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.85 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B88

4b88


Resolution: 2.271→49.408 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 572 4.8 %
Rwork0.1933 --
obs0.1951 11964 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.271→49.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 12 69 2076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052169
X-RAY DIFFRACTIONf_angle_d0.8452970
X-RAY DIFFRACTIONf_dihedral_angle_d13.3271345
X-RAY DIFFRACTIONf_chiral_restr0.045340
X-RAY DIFFRACTIONf_plane_restr0.004403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2709-2.49940.29841390.24592703X-RAY DIFFRACTION96
2.4994-2.86110.30611410.22832824X-RAY DIFFRACTION100
2.8611-3.60450.21871410.19142867X-RAY DIFFRACTION100
3.6045-49.420.20041510.17172998X-RAY DIFFRACTION100
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)
10.20320.17530.05650.44230.04271.16910.04380.1144-0.00230.0105-0.00410.00840.04830.0475-00.33050.0027-0.0190.33410.0180.3215-15.877910.278-20.0806
20.70080.30520.04120.43080.27070.479-0.0103-0.02910.06440.05820.068-0.0298-0.0860.1629-00.36-0.0361-0.00990.30360.00060.3410.429717.9762-13.9367
32.2597-0.7341-0.2818-0.1479-0.28231.30790.01370.03540.12180.0331-0.01480.0337-0.11240.088200.3543-0.03230.00540.2807-0.01390.3538-14.599913.1744-17.338
40.3122-0.1940.12060.09770.11280.6415-0.03590.2245-0.0473-0.0328-0.0168-0.00660.0835-0.1398-00.2886-0.02540.01910.40060.05980.3722-25.26916.6602-27.1904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 27 THROUGH 98 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 99 THROUGH 155 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 156 THROUGH 258 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 259 THROUGH 294 )

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