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- PDB-4tyv: Ensemble refinement of the E502A variant of sacteLam55A from Stre... -

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Basic information

Entry
Database: PDB / ID: 4tyv
TitleEnsemble refinement of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with glucose
ComponentsPutative secreted proteinSecretory protein
KeywordsHYDROLASE / exo-beta-1 / 3-glucanase / beta-1 / GH55 / glucose / secreted / biomass degradation
Function / homologyglucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / glucan catabolic process / Pectin lyase fold / extracellular region / beta-D-glucopyranose / Exo-beta-1,3-glucanase
Function and homology information
Biological speciesStreptomyces sp. SirexAA-E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsBianchetti, C.M. / Takasuka, T.E. / Yik, E.J. / Bergeman, L.F. / Fox, B.G.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Active site and laminarin binding in glycoside hydrolase family 55.
Authors: Bianchetti, C.M. / Takasuka, T.E. / Deutsch, S. / Udell, H.S. / Yik, E.J. / Bergeman, L.F. / Fox, B.G.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Apr 1, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Structure summary
Revision 1.3May 20, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules ..._citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Putative secreted protein
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6588
Polymers118,1672
Non-polymers4906
Water9,062503
1
A: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2083
Polymers59,0841
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4505
Polymers59,0841
Non-polymers3664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.939, 100.055, 99.556
Angle α, β, γ (deg.)90.00, 92.31, 90.00
Int Tables number4
Space group name H-MP1211
Number of models25

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Components

#1: Protein Putative secreted protein / Secretory protein


Mass: 59083.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SirexAA-E (bacteria) / Gene: SACTE_4363 / Plasmid: PVP67K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G2NFJ9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, and 0.010 M MOPS pH 7) mixed in a 1:1 ratio with the Well Solution (20% PEG 3350, 125mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 20% ...Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, and 0.010 M MOPS pH 7) mixed in a 1:1 ratio with the Well Solution (20% PEG 3350, 125mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 20% PEG 3350, 125mM NaCH02, 75mM Glucose, 100mM BTP pH 6.5 and 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 123726 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.2
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.546 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.ENSEMBLE_REFINEMENT: 1.9_1692)refinement
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PEW

4pew


Resolution: 1.75→24.27 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.143 5256 5.01 %
Rwork0.11 --
obs0.112 104912 98.8 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→24.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8339 0 32 503 8874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.21031660.1392892X-RAY DIFFRACTION87
1.7699-1.79070.17491590.12783062X-RAY DIFFRACTION91
1.7907-1.81250.16181680.12183091X-RAY DIFFRACTION93
1.8125-1.83550.15611550.11743230X-RAY DIFFRACTION96
1.8355-1.85960.17551800.11713358X-RAY DIFFRACTION99
1.8596-1.88510.17331700.11283287X-RAY DIFFRACTION100
1.8851-1.9120.16571950.11023343X-RAY DIFFRACTION100
1.912-1.94050.14571660.1033344X-RAY DIFFRACTION100
1.9405-1.97080.14651750.10243345X-RAY DIFFRACTION100
1.9708-2.00310.14821770.09793371X-RAY DIFFRACTION100
2.0031-2.03760.14851880.09123313X-RAY DIFFRACTION100
2.0376-2.07470.14121680.09153433X-RAY DIFFRACTION100
2.0747-2.11460.13421730.09473321X-RAY DIFFRACTION100
2.1146-2.15770.14071750.09393365X-RAY DIFFRACTION100
2.1577-2.20460.14191810.09053330X-RAY DIFFRACTION100
2.2046-2.25580.13611800.09593370X-RAY DIFFRACTION100
2.2558-2.31220.13891600.09093379X-RAY DIFFRACTION100
2.3122-2.37470.14021830.09083357X-RAY DIFFRACTION100
2.3747-2.44450.14191750.09443362X-RAY DIFFRACTION100
2.4445-2.52330.14041740.10153359X-RAY DIFFRACTION100
2.5233-2.61340.13121900.10193351X-RAY DIFFRACTION100
2.6134-2.71790.13561700.09663390X-RAY DIFFRACTION100
2.7179-2.84140.14051770.10073356X-RAY DIFFRACTION100
2.8414-2.9910.12261740.09793391X-RAY DIFFRACTION100
2.991-3.1780.12131770.10313373X-RAY DIFFRACTION100
3.178-3.42270.13351800.10583353X-RAY DIFFRACTION100
3.4227-3.7660.14671730.11363352X-RAY DIFFRACTION100
3.766-4.30830.12371780.12723384X-RAY DIFFRACTION100
4.3083-5.41810.14371830.12213356X-RAY DIFFRACTION98
5.4181-24.26720.18361860.1743438X-RAY DIFFRACTION100

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