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- PDB-4pez: Structure of the E502A variant of sacteLam55A from Streptomyces s... -

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Basic information

Entry
Database: PDB / ID: 4pez
TitleStructure of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritetraose
ComponentsPutative secreted protein
KeywordsHYDROLASE / exo-beta-1 / 3-glucanase / beta-1 / GH55 / laminaritetraose / secreted / biomass degradation
Function / homology
Function and homology information


glucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / glucan catabolic process / extracellular region
Similarity search - Function
: / : / LAM55 pectate lyase-like domain / Pectin lyase fold
Similarity search - Domain/homology
beta-D-glucopyranose / Exo-beta-1,3-glucanase
Similarity search - Component
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.
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
DepositionApr 25, 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
Revision 1.3May 20, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _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 / chem_comp ...atom_site / 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_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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)61,1066
Polymers60,0731
Non-polymers1,0335
Water8,413467
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.)90.00, 99.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative secreted protein


Mass: 60072.637 Da / Num. of mol.: 1 / Fragment: UNP residues 46-605
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: obtained synthetically
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


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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


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


Mass: 18.015 Da / Num. of mol.: 467 / 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 % / Biso Wilson estimate: 20.19 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.565 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.33 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.169 1989 5.02 %
Rwork0.133 --
obs0.135 39630 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4167 0 68 467 4702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074416
X-RAY DIFFRACTIONf_angle_d1.1186040
X-RAY DIFFRACTIONf_dihedral_angle_d12.8691571
X-RAY DIFFRACTIONf_chiral_restr0.048661
X-RAY DIFFRACTIONf_plane_restr0.005801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94760.20741030.15841838X-RAY DIFFRACTION65
1.9476-2.00020.19961060.14882172X-RAY DIFFRACTION75
2.0002-2.05910.2051290.13872411X-RAY DIFFRACTION84
2.0591-2.12550.19961380.14082603X-RAY DIFFRACTION91
2.1255-2.20150.16421580.14262757X-RAY DIFFRACTION96
2.2015-2.28960.20011480.14422794X-RAY DIFFRACTION98
2.2896-2.39370.19031410.13922842X-RAY DIFFRACTION99
2.3937-2.51990.18141550.13772870X-RAY DIFFRACTION99
2.5199-2.67760.1981470.13782861X-RAY DIFFRACTION99
2.6776-2.88420.17831570.13612879X-RAY DIFFRACTION100
2.8842-3.17410.16451500.13482875X-RAY DIFFRACTION100
3.1741-3.63260.15221510.12312908X-RAY DIFFRACTION100
3.6326-4.57350.13241490.11542896X-RAY DIFFRACTION100
4.5735-28.33510.16271570.13612935X-RAY DIFFRACTION100

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