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- PDB-4b88: Ancestral (GNCA) Beta-lactamase class A -

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Basic information

Entry
Database: PDB / ID: 4b88
TitleAncestral (GNCA) Beta-lactamase class A
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGavira, J.A. / Risso, V.A. / Sanchez-Ruiz, J.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Hyperstability and Substrate Promiscuity in Laboratory Resurrections of Precambrian Beta-Lactamases.
Authors: Risso, V.A. / Gavira, J.A. / Mejia-Carmona, D.F. / Gaucher, E.A. / Sanchez-Ruiz, J.M.
History
DepositionAug 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: 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: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1434
Polymers28,0051
Non-polymers1383
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.833, 94.833, 95.340
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 BETA-LACTAMASE


Mass: 28004.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESURRECTED SEQUENCE, ANCESTRAL RECONSTRUCTED. / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESURRECTED PROTEIN. ALA 26 ALA 27 NOT PRESENT IN COORDS RESIDUE NUMBERING IS BASED ON R.P.AMBLER ...RESURRECTED PROTEIN. ALA 26 ALA 27 NOT PRESENT IN COORDS RESIDUE NUMBERING IS BASED ON R.P.AMBLER ET AL. (BIOCHEM. J., V. 276, P. 269, 1991).

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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: 3.83 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growMethod: counter-diffusion / pH: 4
Details: COUNTER-DIFFUSION METHOD. 5.0 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.0

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 18, 2012 / Details: MIRRORS
RadiationMonochromator: OSMIC RIGAKU, MULTILAYER MONOCHROMATOR CMF12-38CU6
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→19.43 Å / Num. obs: 26457 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 19.73 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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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 2QPN

2qpn


Resolution: 2.05→18.659 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 14.26 / Stereochemistry target values: ML
Details: GAPS IN THE COORDINATE FILE ARE FOLLOWING NUMBERING CONVENTION.
RfactorNum. reflection% reflection
Rfree0.1656 1342 5.1 %
Rwork0.1266 --
obs0.1285 26441 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.742 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.2646 Å20 Å20 Å2
2---0.2646 Å20 Å2
3---0.5291 Å2
Refinement stepCycle: LAST / Resolution: 2.05→18.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 9 164 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012102
X-RAY DIFFRACTIONf_angle_d1.3542875
X-RAY DIFFRACTIONf_dihedral_angle_d13.048795
X-RAY DIFFRACTIONf_chiral_restr0.071339
X-RAY DIFFRACTIONf_plane_restr0.007380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12320.20671450.17212481X-RAY DIFFRACTION100
2.1232-2.20810.22481200.15072524X-RAY DIFFRACTION100
2.2081-2.30840.18571280.13492504X-RAY DIFFRACTION100
2.3084-2.42990.16271430.12462495X-RAY DIFFRACTION100
2.4299-2.58180.16011300.11832512X-RAY DIFFRACTION100
2.5818-2.78050.19691400.12992478X-RAY DIFFRACTION100
2.7805-3.05920.18951240.13542535X-RAY DIFFRACTION100
3.0592-3.49940.1621250.12652499X-RAY DIFFRACTION100
3.4994-4.39930.12311430.09682527X-RAY DIFFRACTION100
4.3993-18.660.15561440.13052544X-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)
10.14790.0527-0.08410.1263-0.08090.16580.0525-0.02540.0749-0.1366-0.02730.1429-0.0769-0.0750.02230.14450.0178-0.03070.113-0.03360.161688.134825.8171-25.4377
20.0373-0.0036-0.06090.06380.02930.0941-0.0369-0.0390.01830.02770.0573-0.14370.03340.0898-00.10140.0107-0.0070.1126-0.01450.1365112.16728.1074-18.5956
30.0612-0.0010.03110.0589-0.01860.1035-0.0487-0.1927-0.01140.2010.1088-0.03280.06140.00190.00480.19110.03-0.05080.1645-0.02880.0976109.844811.3664-6.1606
40.1503-0.2546-0.11430.39570.18020.27890.002-0.0026-0.0093-0.03910.0151-0.124-0.0094-0.0124-00.1084-0.00730.00440.1014-0.01730.1127106.130417.0351-22.5014
50.0202-0.064-0.06060.10510.13560.32380.0179-0.05490.01380.073-0.07210.14710.023-0.064-0.00120.1094-0.01080.01310.0998-0.04310.124388.897317.2632-16.655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 28:68)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 69:98)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 99:131)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 132:212)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 213:290)

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