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- PDB-5fqi: W229D and F290W mutant of the last common ancestor of Gram-negati... -

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Basic information

Entry
Database: PDB / ID: 5fqi
TitleW229D and F290W mutant of the last common ancestor of Gram-negative bacteria (GNCA4) beta-lactamase class A
ComponentsGNCA4 LACTAMASE W229D AND F290W
KeywordsHYDROLASE / PRECAMBRIAN / RESURRECTED BETA-LACTAMASE / GNCA4
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGavira, J.A. / Risso, V.A. / Martinez-Rodriguez, S. / 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 1.1Jul 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 / 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 W229D AND F290W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,37617
Polymers28,9711
Non-polymers1,40616
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.962, 46.962, 189.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GNCA4 LACTAMASE W229D AND F290W


Mass: 28970.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: beta-lactamase

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Non-polymers , 7 types, 204 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


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


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsANCESTRAL RECONSTRUCTED MUTANT W229D AND F290W 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: 5
Details: COUNTERDIFFUSION: ACNA 0.1M PH 5.0,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: ID29 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.4→40.67 Å / Num. obs: 46133 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 16.32 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.4
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.7 / % possible all: 99.3

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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: 1.4→40.67 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 16.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1581 2336 5.1 %
Rwork0.1419 --
obs0.1428 46041 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.79 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1987 0 92 188 2267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052266
X-RAY DIFFRACTIONf_angle_d0.9243062
X-RAY DIFFRACTIONf_dihedral_angle_d13.885856
X-RAY DIFFRACTIONf_chiral_restr0.068346
X-RAY DIFFRACTIONf_plane_restr0.006403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.42860.29061230.25982603X-RAY DIFFRACTION99
1.4286-1.45970.25991420.24042561X-RAY DIFFRACTION100
1.4597-1.49370.24381400.21432529X-RAY DIFFRACTION100
1.4937-1.5310.23251310.20772579X-RAY DIFFRACTION100
1.531-1.57240.19841490.18672585X-RAY DIFFRACTION100
1.5724-1.61870.17351290.17192559X-RAY DIFFRACTION99
1.6187-1.67090.15291340.16122562X-RAY DIFFRACTION100
1.6709-1.73070.17851330.1562604X-RAY DIFFRACTION100
1.7307-1.80.18071370.14612578X-RAY DIFFRACTION100
1.8-1.88190.16231540.14082543X-RAY DIFFRACTION100
1.8819-1.98110.141370.13362550X-RAY DIFFRACTION100
1.9811-2.10520.14321190.12682585X-RAY DIFFRACTION100
2.1052-2.26770.15841510.1242572X-RAY DIFFRACTION99
2.2677-2.49590.13141340.1212572X-RAY DIFFRACTION100
2.4959-2.8570.14381410.12182561X-RAY DIFFRACTION100
2.857-3.59920.15541330.12772588X-RAY DIFFRACTION99
3.5992-40.68740.14731490.14292574X-RAY DIFFRACTION99
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)
11.34190.19450.4671.26360.36891.7752-0.0688-0.06480.2126-0.1835-0.07270.2-0.2081-0.2420.08230.11970.0248-0.02690.1173-0.04590.132722.250824.1534-2.1347
21.42870.40150.12392.38410.25171.86510.01-0.0809-0.0410.07890.1039-0.2360.07890.2992-0.11570.10040.0283-0.0180.1947-0.0380.13746.517920.587114.2239
31.3091-0.03710.48050.81360.35391.5846-0.00270.0897-0.0556-0.0660.062-0.06690.0530.1841-0.05470.12040.00160.01720.157-0.02810.1438.576718.39841.4379
40.71010.11160.50651.233-0.50372.5070.0393-0.1983-0.07850.0573-0.0840.10820.3275-0.08570.02630.1552-0.01440.02750.1637-0.00040.141625.85412.69048.4035
53.8928-1.0144-0.84681.41090.8731.0717-0.1022-0.36490.18970.0915-0.05170.193-0.1344-0.27670.07020.11470.01230.00170.2269-0.09280.178823.231828.196311.8571
61.9770.2069-0.2121.6289-0.16071.784-0.0777-0.15470.2936-0.151-0.05180.2179-0.2232-0.21240.08470.13460.0277-0.04290.1673-0.07530.178920.095428.9882.7577
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 118 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 119 THROUGH 179 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 180 THROUGH 212 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 213 THROUGH 238 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 240 THROUGH 293 )

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