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- PDB-5fqq: Last common ancestor of Gram-negative bacteria (GNCA4) beta-lacta... -

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Basic information

Entry
Database: PDB / ID: 5fqq
TitleLast common ancestor of Gram-negative bacteria (GNCA4) beta-lactamase class A
ComponentsGNCA4 LACTAMASE
KeywordsHYDROLASE / PRECAMBRIAN / RESURRECTED BETA-LACTAMASE / GNCA4
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: 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 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
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

Downloads & links

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Assembly

Deposited unit
A: GNCA4 LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2293
Polymers29,0031
Non-polymers2262
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.338, 49.338, 199.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein GNCA4 LACTAMASE


Mass: 29002.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ANCESTRAL RECONSTRUCTED BETA-LACTAMASE CLASS A / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: beta-lactamase
#2: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHISTAG

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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growMethod: counter-diffusion / pH: 5
Details: CAPILLARY COUNTER DIFFUSION: 20%PEG 8K, 0.2M MG ACETATE, 0.1M NA-CACODYLATE PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.12→42.73 Å / Num. obs: 15552 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 58.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.4
Reflection shellResolution: 2.12→2.19 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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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: 2.12→42.73 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 775 5 %
Rwork0.1848 --
obs0.1865 15494 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.65 Å2
Refinement stepCycle: LAST / Resolution: 2.12→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 15 28 2018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082071
X-RAY DIFFRACTIONf_angle_d0.9872823
X-RAY DIFFRACTIONf_dihedral_angle_d12.4311252
X-RAY DIFFRACTIONf_chiral_restr0.055327
X-RAY DIFFRACTIONf_plane_restr0.006375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1203-2.25310.30961360.282476X-RAY DIFFRACTION100
2.2531-2.42710.32161360.24462420X-RAY DIFFRACTION100
2.4271-2.67130.25511310.21052444X-RAY DIFFRACTION100
2.6713-3.05780.22021430.21222449X-RAY DIFFRACTION100
3.0578-3.85210.22491250.20142446X-RAY DIFFRACTION100
3.8521-42.73660.19351040.15512484X-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)
12.39981.5014-1.33625.2788-1.44926.3606-1.22160.3735-1.5207-2.67120.3438-1.76721.96381.43210.50461.06540.45770.29740.90390.16670.779232.124947.6868-8.3955
23.8977-0.2428-0.99255.0802-0.51237.86960.30230.31180.4616-0.6921-0.1582-0.4501-0.25230.7183-0.19010.62110.11880.15090.64330.10430.598525.469759.0865-5.9679
34.5777-0.5487-1.82571.9179-1.39324.38140.6762-0.09690.92790.25910.15010.3175-1.2485-0.5404-0.83820.78390.13950.25040.68850.07150.84045.769766.30111.5439
46.841-1.45440.28327.16711.9457.11760.4073-0.6721-0.68740.18190.01320.89340.1292-0.5887-0.16020.44810.0166-0.00690.80030.21130.73960.208151.90814.7905
54.65250.1146-1.84785.8187-0.96645.88950.2764-0.47650.34330.60770.27050.316-0.7251-0.3164-0.32870.54170.05210.080.74030.07780.60668.95457.585714.5755
62.52131.1946-1.53284.5514-2.84284.27950.60850.50490.7557-0.20890.19010.4755-0.5198-1.0766-0.79050.56140.23960.13210.74770.23760.82434.535465.19383.3166
73.2028-0.0553-1.37247.3024-1.68134.40740.34890.66470.1113-0.75940.16790.37750.0954-1.1827-0.62950.69630.0452-0.09920.98640.23810.71017.235657.8034-5.5146
84.037-0.9529-3.10734.5792-0.17115.78810.3848-0.67640.56930.2837-0.0618-0.4976-0.16290.4487-0.24430.45930.0080.01950.59390.0090.595921.352460.89748.6041
95.08782.5682-0.02878.20260.35878.04270.1489-0.40430.1327-0.4063-0.3754-0.20080.46970.45710.13590.54790.1474-0.00160.58210.06920.625923.665554.3412.0859
108.75044.4531-0.75312.9576-0.91667.55220.4647-0.3837-0.2721-0.3972-0.5104-0.6220.83390.98880.12880.63250.25620.12230.76080.22220.825529.795348.72551.9813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 27 THROUGH 40 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 41 THROUGH 68 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 69 THROUGH 98 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 99 THROUGH 118 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 119 THROUGH 131 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 132 THROUGH 155 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 156 THROUGH 179 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 180 THROUGH 238 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 240 THROUGH 271 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 272 THROUGH 291 )

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