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- PDB-4tz3: Ensemble refinement of the E502A variant of sacteLam55A from Stre... -

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Basic information

Entry
Database: PDB / ID: 4tz3
TitleEnsemble refinement of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritetraose
ComponentsPutative secreted proteinSecretory protein
KeywordsHYDROLASE / exo-beta-1 / 3-glucanase / beta-1 / GH55 / laminaritetraose / 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: 1.9 Å
AuthorsBianchetti, C.M. / Takasuka, T.E. / Yik, E.J. / Bergeman, L.F. / Fox, B.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-07ER64494 United States
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: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / 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_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
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 / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9176
Polymers58,8841
Non-polymers1,0335
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.276, 100.210, 54.223
Angle α, β, γ (deg.)90.000, 99.460, 90.000
Int Tables number4
Space group name H-MP1211
Number of models25

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Components

#1: Protein Putative secreted protein / Secretory protein


Mass: 58884.359 Da / Num. of mol.: 1 / Fragment: UNP residues 57-605
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: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
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 (22% PEG 3350, 50mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 22% ...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 (22% PEG 3350, 50mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 22% PEG 3350, 50mM NaCH02, 25mM laminaritetraose, 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
ReflectionRedundancy: 3.9 % / Number: 191860 / Rmerge(I) obs: 0.095 / Χ2: 0.91 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 49764 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.885010.0410.2963.9
3.884.8810.0450.3934
3.393.8810.0610.6614
3.083.3910.0820.9414
2.863.0810.0910.9174
2.692.8610.1141.0773.9
2.552.6910.1281.0763.9
2.442.5510.1451.1153.9
2.352.4410.1621.143.9
2.272.3510.1691.1253.8
2.22.2710.1921.0983.8
2.132.210.2091.133.8
2.082.1310.2291.0673.8
2.032.0810.2511.0563.8
1.982.0310.2790.9983.8
1.941.9810.3210.9473.7
1.91.9410.3580.8983.8
1.861.910.4150.8273.7
1.831.8610.4870.7563.7
1.81.8310.5650.713.7
ReflectionResolution: 1.8→50 Å / Num. obs: 49764 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.095 / Χ2: 0.908 / Net I/av σ(I): 11.767 / Net I/σ(I): 7.3 / Num. measured all: 191860
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.833.70.56524650.7198.9
1.83-1.863.70.48724820.75698.6
1.86-1.93.70.41524510.82798.7
1.9-1.943.80.35824700.89898.4
1.94-1.983.70.32124730.94799.2
1.98-2.033.80.27924630.99899.1
2.03-2.083.80.25125001.05699
2.08-2.133.80.22924521.06798.9
2.13-2.23.80.20924781.1399.2
2.2-2.273.80.19224631.09898.7
2.27-2.353.80.16925101.12598.9
2.35-2.443.90.16224641.1499
2.44-2.553.90.14524881.11599.4
2.55-2.693.90.12824861.07699
2.69-2.863.90.11425071.07799.4
2.86-3.0840.09124860.917100
3.08-3.3940.08225240.941100
3.39-3.8840.06125350.661100
3.88-4.8840.04525110.39399.7
4.88-503.90.04125560.29699.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4pew


Resolution: 1.9→28.332 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 14.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1513 1989 5.02 %
Rwork0.1131 37643 -
obs0.1151 39632 93.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso min: 99999 Å2
Refinement stepCycle: final / Resolution: 1.9→28.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4167 0 0 0 4167
Num. residues----0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94760.19371030.11391838194165
1.9476-2.00020.1731060.11482172227875
2.0002-2.05910.18521290.11212411254084
2.0591-2.12550.19661380.11122603274191
2.1255-2.20150.16431580.10842757291596
2.2015-2.28960.16891480.10762794294298
2.2896-2.39370.151410.09752842298399
2.3937-2.51990.15271550.09482870302599
2.5199-2.67760.16311470.09552861300899
2.6776-2.88420.14461570.102228793036100
2.8842-3.17410.15281500.110528753025100
3.1741-3.63260.15191510.110429083059100
3.6326-4.57350.11661490.115628963045100
4.5735-28.33510.15021570.143129373094100

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