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- PDB-4c6y: Ancestral PNCA (last common ancestors of Gram-positive and Gram- ... -

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Basic information

Entry
Database: PDB / ID: 4c6y
TitleAncestral PNCA (last common ancestors of Gram-positive and Gram- negative bacteria) beta-lactamase class A
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsGavira, J.A. / Risso, V.A. / Sanchez-Ruiz, J.M.
Citation
Journal: Proteins / Year: 2014
Title: Phenotypic Comparisons of Consensus Variants Versus Laboratory Resurrections of Precambrian Proteins.
Authors: Risso, V.A. / Gavira, J.A. / Gaucher, E.A. / Sanchez-Ruiz, J.M.
#1: Journal: 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
DepositionSep 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 2.0Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,08631
Polymers56,1772
Non-polymers2,90929
Water5,459303
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,86019
Polymers28,0891
Non-polymers1,77118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,22612
Polymers28,0891
Non-polymers1,13811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.581, 57.473, 240.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA-LACTAMASE /


Mass: 28088.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Description: RESURRECTED SEQUENCE, ANCESTRAL RECONSTRUCTED / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: beta-lactamase

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Non-polymers , 7 types, 332 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESURRECTED SEQUENCE, ANCESTRAL RECONSTRUCTED

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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: 7
Details: CAPILLARY COUNTERDIFFUSION 20%PEG 400, 15%PEG 4K, 10% PEG 8K, TRIS-HCL 0.1M PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→46.7 Å / Num. obs: 52107 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 20.14 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.3 / % possible all: 99

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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: 1.799→46.703 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 14.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.17 2660 5.1 %
Rwork0.1416 --
obs0.143 52085 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.9 Å2
Refinement stepCycle: LAST / Resolution: 1.799→46.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 190 303 4427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014437
X-RAY DIFFRACTIONf_angle_d1.3025992
X-RAY DIFFRACTIONf_dihedral_angle_d14.7891756
X-RAY DIFFRACTIONf_chiral_restr0.049673
X-RAY DIFFRACTIONf_plane_restr0.006783
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7993-1.83210.25241380.19492462X-RAY DIFFRACTION98
1.8321-1.86730.22351370.16442554X-RAY DIFFRACTION100
1.8673-1.90540.19011730.14542525X-RAY DIFFRACTION100
1.9054-1.94680.15271250.14412571X-RAY DIFFRACTION100
1.9468-1.99210.18711250.13962627X-RAY DIFFRACTION100
1.9921-2.04190.1661340.12842544X-RAY DIFFRACTION100
2.0419-2.09720.17411340.12652577X-RAY DIFFRACTION100
2.0972-2.15890.14251490.12572555X-RAY DIFFRACTION100
2.1589-2.22860.17811410.12212584X-RAY DIFFRACTION100
2.2286-2.30820.16891430.12852582X-RAY DIFFRACTION100
2.3082-2.40060.14541440.1192589X-RAY DIFFRACTION100
2.4006-2.50990.17491340.12232603X-RAY DIFFRACTION100
2.5099-2.64220.16971530.11582601X-RAY DIFFRACTION100
2.6422-2.80770.14471420.12622594X-RAY DIFFRACTION100
2.8077-3.02440.14711440.13392627X-RAY DIFFRACTION100
3.0244-3.32870.17061250.14032639X-RAY DIFFRACTION100
3.3287-3.81020.15541220.14362656X-RAY DIFFRACTION100
3.8102-4.79970.15621470.14152699X-RAY DIFFRACTION100
4.7997-46.71860.2171500.18792836X-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)
13.73981.363-0.9491.7787-0.57891.81690.1281-0.48010.03250.3726-0.1585-0.2008-0.01760.18480.0320.1514-0.0211-0.0440.1767-0.00660.1607-6.78485.2519-33.1233
21.69411.86950.41832.26190.43140.11940.2317-0.32940.28070.257-0.17910.2678-0.0149-0.146-0.08760.1243-0.00820.00750.1938-0.01980.1969-16.34089.651-37.2391
31.3135-0.0970.11071.0849-0.08741.79080.02680.10810.053-0.2449-0.09670.09480.0131-0.09220.0810.17550.0167-0.02040.08220.00820.1764-22.51929.759-64.8489
42.21680.57260.40881.7571-0.2671.96060.1393-0.085-0.0829-0.4316-0.2791-0.39730.39790.46930.1170.25910.10990.0670.22580.06770.2362-8.40365.9781-70.5761
51.0646-0.00170.20941.0323-0.11371.12950.0154-0.01980.1028-0.0682-0.0457-0.0192-0.04280.03390.0390.1060.00920.00130.09490.00940.1604-17.718711.6533-55.1052
60.4402-0.7061-0.16141.8793-1.11733.67220.065-0.067-0.0449-0.0547-0.06770.07790.4203-0.03510.00250.129-0.017-0.00550.10120.00220.1747-12.1791-3.8864-49.0819
72.0702-0.0017-0.56160.9517-0.40591.3307-0.057-0.05330.0496-0.02670.07690.00650.17720.039-0.01870.1083-0.0094-0.01710.0953-0.00090.1303-9.47761.1351-42.884
85.39710.9648-0.34662.5547-0.74752.1731-0.23120.0841-0.7592-0.2032-0.0742-0.21740.91430.05790.22150.8038-0.10330.070.18490.01130.2598-21.2463-28.4798-36.5916
91.5953-0.4150.84411.4037-0.0272.3643-0.03230.0283-0.0601-0.30390.051-0.22060.61570.3213-0.03230.36120.01380.04780.24150.01080.1721-17.1443-17.7786-31.3385
101.0133-0.6437-1.42640.92210.013.99960.1265-0.39080.0880.15030.00590.0994-0.08120.0364-0.12920.2051-0.04460.01430.3292-0.00090.1686-26.794-6.4614-6.0073
111.82950.4947-0.98361.0995-0.42913.17540.0031-0.14710.02780.00290.04940.09030.0548-0.0059-0.04460.135-0.01060.00110.19030.0150.1228-25.0026-6.8565-19.3048
120.77370.1609-0.9141.6906-0.12412.5535-0.1119-0.1932-0.24170.0201-0.0263-0.15151.03240.31370.0580.43340.08440.03310.28260.07240.1834-18.8846-20.8447-18.2245
133.4693-0.61160.23223.0063-1.31021.71910.2046-0.102-0.3827-0.0528-0.0206-0.20370.79930.15260.15831.1363-0.0390.11060.12990.11720.1913-22.1931-29.4453-26.0807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 26 THROUGH 50 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 51 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 212 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 213 THROUGH 238 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 240 THROUGH 290 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 27 THROUGH 40 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 41 THROUGH 68 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 69 THROUGH 118 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 119 THROUGH 195 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 196 THROUGH 271 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 272 THROUGH 290 )

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