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- PDB-4uhu: W229D mutant of the last common ancestor of Gram-negative bacteri... -

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Basic information

Entry
Database: PDB / ID: 4uhu
TitleW229D mutant of the last common ancestor of Gram-negative bacteria (GNCA) beta-lactamase class A
ComponentsGNCA LACTAMASE W229D
KeywordsHYDROLASE / PRECAMBRIAN / RESURRECTED BETA-LACTAMASE / GNCA
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: 1.305 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
DepositionMar 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 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_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.page_first ..._citation.country / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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

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Assembly

Deposited unit
A: GNCA LACTAMASE W229D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0196
Polymers28,7621
Non-polymers2565
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.138, 50.568, 69.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2146-

HOH

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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) / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: beta-lactamase
#2: Chemical ChemComp-FMT / FORMIC ACID


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIT IS AN ANCESTRAL RECONSTRUCTED. THERE IS A MUTATION AT POSITION 229.

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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: 4
Details: COUNTERDIFFUSION METHOD: 5.0 M NAFORMATE, 0.1 M NAAC PH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97779
DetectorType: DECTRIS HPADS / Date: Nov 14, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 1.3→26.63 Å / Num. obs: 60121 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 12.63 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9
Reflection shellResolution: 1.31→1.31 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.2 / % possible all: 94.8

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Processing

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

4b88


Resolution: 1.305→26.632 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1791 3043 5.1 %
Rwork0.1619 --
obs0.1628 60130 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.2 Å2
Refinement stepCycle: LAST / Resolution: 1.305→26.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 17 265 2272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062199
X-RAY DIFFRACTIONf_angle_d1.1283008
X-RAY DIFFRACTIONf_dihedral_angle_d12.052837
X-RAY DIFFRACTIONf_chiral_restr0.041345
X-RAY DIFFRACTIONf_plane_restr0.005407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3048-1.32520.3291270.30292446X-RAY DIFFRACTION94
1.3252-1.34690.26981390.27172494X-RAY DIFFRACTION97
1.3469-1.37010.26441290.26212598X-RAY DIFFRACTION99
1.3701-1.3950.28491290.2522542X-RAY DIFFRACTION98
1.395-1.42180.25221340.23172541X-RAY DIFFRACTION99
1.4218-1.45090.23861390.21312590X-RAY DIFFRACTION99
1.4509-1.48240.19051410.18392572X-RAY DIFFRACTION99
1.4824-1.51690.16751160.162590X-RAY DIFFRACTION99
1.5169-1.55480.18711400.15342557X-RAY DIFFRACTION99
1.5548-1.59690.17321630.14712567X-RAY DIFFRACTION99
1.5969-1.64380.16461290.15192529X-RAY DIFFRACTION97
1.6438-1.69690.16881340.15172625X-RAY DIFFRACTION100
1.6969-1.75750.20141410.15362607X-RAY DIFFRACTION99
1.7575-1.82790.17731310.15142610X-RAY DIFFRACTION100
1.8279-1.9110.18361350.15342641X-RAY DIFFRACTION100
1.911-2.01180.15751390.14832626X-RAY DIFFRACTION100
2.0118-2.13780.1651540.13852610X-RAY DIFFRACTION100
2.1378-2.30270.15121540.14712567X-RAY DIFFRACTION97
2.3027-2.53430.19581380.1592672X-RAY DIFFRACTION100
2.5343-2.90060.20671420.16312650X-RAY DIFFRACTION99
2.9006-3.6530.17471610.15092664X-RAY DIFFRACTION99
3.653-26.63760.14271280.15582789X-RAY DIFFRACTION98
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)
10.94050.0159-0.14251.0390.29310.7539-0.003-0.0715-0.18870.2515-0.02030.07010.1484-0.08270.01030.135-0.02620.00690.10220.02020.1168.3145101.829328.1427
20.65020.19860.05590.9035-0.03280.9462-0.05370.06610.0656-0.07010.0047-0.0142-0.10630.03390.04960.0907-0.0018-0.01090.11670.01530.103913.1334124.51357.4198
32.2203-0.2241-0.28881.5937-0.214.0867-0.0913-0.11530.20880.17050.0154-0.284-0.16790.34650.07170.1241-0.0322-0.05370.14780.02810.174626.2043130.385415.3524
40.7166-0.02140.01240.8276-0.32830.7647-0.0221-0.0618-0.01290.0433-0.01070.0269-0.0633-0.03120.03070.07720.0091-0.01210.08840.00230.09389.8491120.74817.9229
50.8341-0.2298-0.15921.1538-0.18581.1733-0.0140.0132-0.07430.0267-0.0452-0.09720.0730.10070.06090.06440.0025-0.00160.0756-0.00520.100517.0739107.794816.3899
62.38551.34641.34385.07062.78483.66280.11620.0264-0.2553-0.0011-0.0943-0.0850.2615-0.0277-0.01870.1820.0161-0.03890.10360.01190.139318.251297.360725.6085
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 98 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 99 THROUGH 118 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 119 THROUGH 194 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 195 THROUGH 271 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 272 THROUGH 294 )

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