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- PDB-5fqm: Last common ancestor of Gram Negative Bacteria (GNCA) Class A bet... -

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Basic information

Entry
Database: PDB / ID: 5fqm
TitleLast common ancestor of Gram Negative Bacteria (GNCA) Class A beta- lactamase
ComponentsGNCA BETA LACTAMASE
KeywordsHYDROLASE / PRECAMBRIAN / RESURRECTED BETA-LACTAMASE / GNCA
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMartinez Rodriguez, S. / Gavira, J.A. / 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 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jan 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: GNCA BETA LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,07413
Polymers28,9651
Non-polymers1,10912
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.230, 94.230, 93.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein GNCA BETA LACTAMASE


Mass: 28964.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: RESURRECTED SEQUENCE, ANCESTRAL RECONSTRUCTED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS ENTRY IS RELEATED TO PDB ENTRIES 4UHU AND 4B88

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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: 3.44 Å3/Da / Density % sol: 64.32 % / Description: NONE
Crystal growpH: 8 / Details: 2.0M NH4SO4, 0.1M TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.02
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.5→21.07 Å / Num. obs: 59525 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 3.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.1 / % possible all: 95.7

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Processing

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

4b88


Resolution: 1.5→21.07 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 3112 5.2 %
Rwork0.176 --
obs0.1772 59484 91.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→21.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 71 311 2358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012227
X-RAY DIFFRACTIONf_angle_d1.393027
X-RAY DIFFRACTIONf_dihedral_angle_d15.316842
X-RAY DIFFRACTIONf_chiral_restr0.057337
X-RAY DIFFRACTIONf_plane_restr0.007401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52350.27441680.25552773X-RAY DIFFRACTION99
1.5235-1.54840.2713870.24831735X-RAY DIFFRACTION62
1.5484-1.57510.29541510.25612739X-RAY DIFFRACTION99
1.5751-1.60380.24531530.22722789X-RAY DIFFRACTION99
1.6038-1.63460.2361670.21252769X-RAY DIFFRACTION100
1.6346-1.66790.25521760.20332785X-RAY DIFFRACTION100
1.6679-1.70420.2491480.19512790X-RAY DIFFRACTION99
1.7042-1.74380.22331170.18952820X-RAY DIFFRACTION100
1.7438-1.78740.21931730.18422749X-RAY DIFFRACTION99
1.7874-1.83570.19081400.1752824X-RAY DIFFRACTION100
1.8357-1.88970.18541150.17712518X-RAY DIFFRACTION99
1.8897-1.95060.1759760.16851375X-RAY DIFFRACTION60
1.9506-2.02030.1692880.16542264X-RAY DIFFRACTION100
2.0203-2.10110.1848830.16632246X-RAY DIFFRACTION79
2.1011-2.19670.21042150.16432749X-RAY DIFFRACTION99
2.1967-2.31230.17771380.17142233X-RAY DIFFRACTION80
2.3123-2.4570.17582140.17292746X-RAY DIFFRACTION100
2.457-2.64640.1661070.17362853X-RAY DIFFRACTION100
2.6464-2.91210.21021400.17032542X-RAY DIFFRACTION90
2.9121-3.3320.21281630.16882799X-RAY DIFFRACTION100
3.332-4.19260.17561580.14862397X-RAY DIFFRACTION85
4.1926-21.07250.18561350.17772877X-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)
10.13120.074-0.18630.1352-0.01590.16110.0380.02260.0136-0.2764-0.0030.1268-0.1462-0.05850.07580.16740.0247-0.05610.1035-0.01930.1552-7.59225.2182-7.141
20.30530.246-0.08420.25790.0530.1222-0.1323-0.16770.00990.11370.129-0.05440.05620.13770.00670.15940.0661-0.00810.1701-0.00710.101617.614110.46746.5647
30.4545-0.2077-0.22690.52110.27220.3578-0.0333-0.0475-0.0149-0.01550.0083-0.01180.02810.033-0.0020.1080.00680.00570.0913-0.00820.09046.173915.1488-0.8701
40.114-0.1006-0.09160.19-0.12880.2582-0.01050.0230.0302-0.0672-0.01790.1517-0.0473-0.10910.1410.09930.0008-0.00390.1069-0.04120.1384-8.979121.70451.0731
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 118 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 119 THROUGH 258 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 259 THROUGH 292 )

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