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- PDB-6z1h: Ancestral glycosidase (family 1) -

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Basic information

Entry
Database: PDB / ID: 6z1h
TitleAncestral glycosidase (family 1)
Components
  • (Residues 249 to 266 of chain A and 246 to 258 of chain B could not be identified and has been ...) x 2
  • ANCESTRAL RECONSTRUCTED GLYCOSIDASE
KeywordsHYDROLASE / Ancestral reconstructed / glycosidase / Family 1
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGavira, J.A. / Risso, V.A. / Sanchez-Ruiz, J.M. / Gamiz-Arco, G. / Gutierrez-Rus, L. / Ibarra-Molero, B. / Hoshino, Y. / Petrovic, D. / Romero-Rivera, A. / Seelig, B. ...Gavira, J.A. / Risso, V.A. / Sanchez-Ruiz, J.M. / Gamiz-Arco, G. / Gutierrez-Rus, L. / Ibarra-Molero, B. / Hoshino, Y. / Petrovic, D. / Romero-Rivera, A. / Seelig, B. / Kamerlin, S.C.L. / Gaucher, E.A.
Funding support United States, Spain, 2items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0041/2017 United States
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-74875-P Spain
Citation
Journal: Nat Commun / Year: 2021
Title: Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase.
Authors: Gamiz-Arco, G. / Gutierrez-Rus, L.I. / Risso, V.A. / Ibarra-Molero, B. / Hoshino, Y. / Petrovic, D. / Justicia, J. / Cuerva, J.M. / Romero-Rivera, A. / Seelig, B. / Gavira, J.A. / Kamerlin, ...Authors: Gamiz-Arco, G. / Gutierrez-Rus, L.I. / Risso, V.A. / Ibarra-Molero, B. / Hoshino, Y. / Petrovic, D. / Justicia, J. / Cuerva, J.M. / Romero-Rivera, A. / Seelig, B. / Gavira, J.A. / Kamerlin, S.C.L. / Gaucher, E.A. / Sanchez-Ruiz, J.M.
#1: Journal: Biorxiv / Year: 2020
Title: Novel heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase
Authors: Gamiz-Arco, G. / Gutierrez-Rus, L. / Risso, V.A. / Ibarra-Molero, B. / Hoshino, Y. / Petrovic, D. / Romero-Rivera, A. / Seelig, B. / Gavira, J.A. / Kamerlin, S.C.L. / Gaucher, E.A. / Sanchez-Ruiz, J.M.
History
DepositionMay 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jan 27, 2021Group: Database references / Category: citation / citation_author
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANCESTRAL RECONSTRUCTED GLYCOSIDASE
B: ANCESTRAL RECONSTRUCTED GLYCOSIDASE
C: Residues 249 to 266 of chain A and 246 to 258 of chain B could not be identified and has been included as UNK in chain C and D, respectively.
D: Residues 249 to 266 of chain A and 246 to 258 of chain B could not be identified and has been included as UNK in chain C and D, respectively.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2368
Polymers107,8954
Non-polymers3404
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-41 kcal/mol
Surface area30870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.263, 80.668, 97.808
Angle α, β, γ (deg.)90.000, 100.061, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ANCESTRAL RECONSTRUCTED GLYCOSIDASE


Mass: 52610.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Residues 249 to 266 of chain A and 246 to 258 of chain B could not be identified and has been ... , 2 types, 2 molecules CD

#2: Protein/peptide Residues 249 to 266 of chain A and 246 to 258 of chain B could not be identified and has been included as UNK in chain C and D, respectively.


Mass: 1549.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein/peptide Residues 249 to 266 of chain A and 246 to 258 of chain B could not be identified and has been included as UNK in chain C and D, respectively.


Mass: 1124.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 38 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: HR1 (#C41): 0.1 M HEPES Na pH 7.5, 10% v/v 2-Propanol, 20% w/v PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2019
RadiationMonochromator: Si(100) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→48.15 Å / Num. obs: 27987 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 59.93 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3063 / CC1/2: 0.707 / % possible all: 97.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J78

2j78


Resolution: 2.5→48.15 Å / SU ML: 0.3373 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2952
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 1405 5.05 %
Rwork0.1939 26413 -
obs0.1964 27818 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6156 0 176 34 6366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346751
X-RAY DIFFRACTIONf_angle_d0.66269176
X-RAY DIFFRACTIONf_chiral_restr0.045936
X-RAY DIFFRACTIONf_plane_restr0.00361203
X-RAY DIFFRACTIONf_dihedral_angle_d6.13125356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.33741550.27632618X-RAY DIFFRACTION99.93
2.59-2.690.34811230.25362634X-RAY DIFFRACTION100
2.69-2.820.31011350.24692622X-RAY DIFFRACTION99.89
2.82-2.960.28551330.23452629X-RAY DIFFRACTION100
2.96-3.150.28821320.22312632X-RAY DIFFRACTION99.96
3.15-3.390.28221580.20792629X-RAY DIFFRACTION100
3.39-3.730.2791510.1912637X-RAY DIFFRACTION99.82
3.73-4.270.19071330.16882638X-RAY DIFFRACTION99.93
4.27-5.380.21321400.16492670X-RAY DIFFRACTION100
5.38-48.150.21731450.18952704X-RAY DIFFRACTION99.89
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)
14.350053090951.274744136690.4343940278042.54332203609-0.2074322866382.30873700502-0.3596659732430.0501875447955-0.498263736146-0.168729382840.143767119125-0.4335267824810.206909767242-0.01251823104590.1589859475540.366103904981-0.05254553597420.04442350577650.331672995988-0.008798123419860.4543038092926.55582890112.251606773224.5483431324
23.969171859441.235033414710.2753929656873.599757806670.9992990874783.05018761934-0.3428174803880.859929923868-0.949268989045-0.597871387820.328639619229-0.7816949612780.2837513234860.235989174379-0.07235760458370.745959511497-0.2624685245660.2465503983320.711641183766-0.1816471399840.72434950514430.6522797192-0.3171422317919.63973208836
33.58321742070.109993806094-1.307785598410.0720853099653-0.2182730135360.5002369694420.1386829052061.24534602372-0.319776912143-0.192254019116-0.0773935332538-0.3723051060580.175350852453-0.312576748351-0.07939921337921.19610946947-0.2649322298070.2584265818181.04797029936-0.2624615672680.82034368662524.7907162739-1.538568068973.72291276168
42.680928198860.8711126332350.03017959420513.58383099512-0.4418672097442.78781103659-0.525050625740.547860143903-0.456707885478-0.7241035384650.5164834993010.1907391831050.321143195139-0.706507169910.04266538878910.583474879392-0.30639936522-0.03227057952280.769718560371-0.009457185160080.5322159670947.80964486304-2.4707013272519.4867463663
52.670288749310.3515369379720.07791996680352.42746159570.6288850272113.941687291950.08030353412780.2850560713390.211538423095-0.7352227651250.1193043347830.12698436573-0.761808972705-0.0487878626767-0.1455765005730.616931131141-0.0531304685025-0.02246183443290.3793093899480.05292335233270.43751541649735.24663881437.27932438526.0621157737
63.36639874689-0.150496072530.05398872430264.864721989930.08583902654592.738546332760.407003323712-0.1561939780440.134499471965-0.677594556921-0.0561292488479-0.546404541918-0.2461373521990.326646070135-0.2837181946460.933847691223-0.2228520313330.1965506072450.692119604125-0.1345167197590.69505754373849.117841845139.191535926725.5417486217
71.28913609348-0.0809586427925-0.4018081240221.485679305640.8177932570332.570826810960.5605955225950.2245634858670.525025126893-0.764722111229-0.15753699742-0.503653397253-1.120941445731.50056854824-0.2632307304891.03527864172-0.2529156229560.3032638321460.990579523387-0.06087584639430.82273783276953.227674948844.11633833824.4954936877
82.68518965599-0.1717627307960.4820887917891.289139077821.096201716952.91391094534-0.0615158482286-0.5152014631920.202654421716-0.2177480968010.492293366715-0.392343908078-0.7150968819490.568454607706-0.2911837313220.505259429799-0.1536897257370.07454468514080.546766778757-0.1954382597830.55708757710543.962723433541.810690575944.9368293907
90.3404667319910.0988517913578-0.6399106859720.2372581435780.009852854119151.38257090480.263308308579-0.1477082723980.135586135255-0.02749753482630.4802906686160.486459381392-0.0773207393540.301012909422-0.5275499007753.09259831937-0.7562896818340.6009459303321.769384255710.09966019201151.296232349458.226139790555.623062464753.2535113682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 191 )
2X-RAY DIFFRACTION2chain 'A' and (resid 192 through 251 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 323 )
4X-RAY DIFFRACTION4chain 'A' and (resid 324 through 451 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 216 )
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 251 )
7X-RAY DIFFRACTION7chain 'B' and (resid 252 through 359 )
8X-RAY DIFFRACTION8chain 'B' and (resid 360 through 450 )
9X-RAY DIFFRACTION9chain 'B' and (resid 451 through 454 )

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