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

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Basic information

Entry
Database: PDB / ID: 4pey
TitleStructure of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminaritriose
ComponentsPutative secreted protein
KeywordsHYDROLASE / exo-beta-1 / 3-glucanase / beta-1 / GH55 / laminaritriose / secreted / biomass degradation
Function / homologyglucan exo-1,3-beta-glucosidase activity / glucan 1,3-beta-glucosidase / glucan catabolic process / Pectin lyase fold / extracellular region / Exo-beta-1,3-glucanase
Function and homology information
Biological speciesStreptomyces sp. SirexAA-E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Sep 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

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Assembly

Deposited unit
A: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0823
Polymers60,0731
Non-polymers1,0092
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.775, 100.195, 53.862
Angle α, β, γ (deg.)90.00, 103.49, 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


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
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, 75mM NaCH02, and 100mM BTP pH 6.0). 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, 75mM NaCH02, and 100mM BTP pH 6.0). Cryoprotected with 20% PEG 3350, 75mM NaCH02, 25mM laminaritriose, 100mM BTP pH 6.0 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: 395273 / Rmerge(I) obs: 0.065 / Χ2: 0.94 / D res high: 1.4 Å / D res low: 50 Å / Num. obs: 100816 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
3.85010.030.3583.9
3.023.810.0370.5614
2.633.0210.0520.8964
2.392.6310.0651.0974
2.222.3910.071.0854
2.092.2210.0791.1394
1.992.0910.0911.2334
1.91.9910.1071.3384
1.831.910.1251.2974
1.761.8310.1421.1914
1.711.7610.1631.0924
1.661.7110.1821.0044
1.621.6610.2040.9964
1.581.6210.2230.913.9
1.541.5810.2490.8853.9
1.511.5410.280.8183.9
1.481.5110.3260.7563.9
1.451.4810.3650.7033.9
1.421.4510.4250.6573.6
1.41.4210.4810.6283.3
ReflectionResolution: 1.4→50 Å / Num. obs: 100816 / % possible obs: 100 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.55 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.481 / % possible all: 99.9

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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
Starting model: 4PEW

4pew


Resolution: 1.5→24.23 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.144 4085 5.02 %Random selection
Rwork0.115 ---
obs0.116 81427 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4167 0 68 562 4797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064503
X-RAY DIFFRACTIONf_angle_d1.136180
X-RAY DIFFRACTIONf_dihedral_angle_d12.3061633
X-RAY DIFFRACTIONf_chiral_restr0.047682
X-RAY DIFFRACTIONf_plane_restr0.006819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51770.19091140.11562386X-RAY DIFFRACTION89
1.5177-1.53620.17771530.11312540X-RAY DIFFRACTION96
1.5362-1.55560.16211290.10952635X-RAY DIFFRACTION99
1.5556-1.57610.16281510.10632643X-RAY DIFFRACTION100
1.5761-1.59770.17161390.10472697X-RAY DIFFRACTION100
1.5977-1.62050.16781320.10722680X-RAY DIFFRACTION100
1.6205-1.64470.16211440.10522673X-RAY DIFFRACTION100
1.6447-1.67030.18031430.10912673X-RAY DIFFRACTION100
1.6703-1.69770.17431500.10362695X-RAY DIFFRACTION100
1.6977-1.7270.15361260.10472674X-RAY DIFFRACTION100
1.727-1.75840.15571340.10262649X-RAY DIFFRACTION100
1.7584-1.79220.15491620.09942701X-RAY DIFFRACTION100
1.7922-1.82880.15741410.09852673X-RAY DIFFRACTION100
1.8288-1.86850.15811320.09922676X-RAY DIFFRACTION100
1.8685-1.9120.14161400.09942687X-RAY DIFFRACTION100
1.912-1.95980.13281400.09312685X-RAY DIFFRACTION100
1.9598-2.01270.1411470.09922660X-RAY DIFFRACTION100
2.0127-2.07190.13261430.10262725X-RAY DIFFRACTION100
2.0719-2.13880.1621440.10752647X-RAY DIFFRACTION100
2.1388-2.21510.14311390.10812658X-RAY DIFFRACTION100
2.2151-2.30380.15241360.1142709X-RAY DIFFRACTION100
2.3038-2.40850.13081420.11962665X-RAY DIFFRACTION100
2.4085-2.53540.1621380.12532718X-RAY DIFFRACTION100
2.5354-2.6940.15191520.13092680X-RAY DIFFRACTION100
2.694-2.90170.13181430.12962696X-RAY DIFFRACTION100
2.9017-3.19320.13851420.12992681X-RAY DIFFRACTION100
3.1932-3.65390.13631430.11422679X-RAY DIFFRACTION100
3.6539-4.59830.11181440.10642726X-RAY DIFFRACTION100
4.5983-24.22920.14551420.13972731X-RAY DIFFRACTION100

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