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- PDB-4pew: Structure of sacteLam55A from Streptomyces sp. SirexAA-E -

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Basic information

Entry
Database: PDB / ID: 4pew
TitleStructure of sacteLam55A from Streptomyces sp. SirexAA-E
ComponentsPutative secreted proteinSecretory protein
KeywordsHYDROLASE / beta-1 / 3-glucanase / secreted / biomass degradation / GH55 / exo-beta-1
Function / homologyglucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / 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 / SAD / Resolution: 1.51 Å
AuthorsBianchetti, C.M. / Takasuka, T.E. / 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 1.2May 20, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_symm_contact / 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_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative secreted protein
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7716
Polymers120,6372
Non-polymers1354
Water25,7071427
1
A: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3673
Polymers60,3181
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4053
Polymers60,3181
Non-polymers862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.967, 92.567, 198.304
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative secreted protein / Secretory protein


Mass: 60318.254 Da / Num. of mol.: 2 / 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): B834 / References: UniProt: G2NFJ9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1427 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
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 (23% PEG 3350, 200mM MgCl2, and 100mM BTP pH 7.0). Cryoprotected with 23% ...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 (23% PEG 3350, 200mM MgCl2, and 100mM BTP pH 7.0). Cryoprotected with 23% PEG 3350, 200mM MgCl2,100mM BTP pH 7.0, 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: Nov 13, 2012 / 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: 11.5 % / Number: 1641294 / Rmerge(I) obs: 0.058 / Χ2: 1.69 / D res high: 1.51 Å / D res low: 50 Å / Num. obs: 142188 / % possible obs: 90.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.15010.0373.27113.2
3.254.110.0392.27412.6
2.843.2510.0522.63811.8
2.582.8410.0582.33311.4
2.42.5810.0662.23311.1
2.262.410.0662.02410.8
2.142.2610.0711.98310.6
2.052.1410.0812.02110.6
1.972.0510.0891.87110.7
1.91.9710.0961.58610.9
1.841.910.1051.33611.3
1.791.8410.1181.19911.6
1.741.7910.1341.0812
1.71.7410.1531.02912.2
1.661.710.180.97112.4
1.631.6610.1980.9412.6
1.591.6310.2150.9312.6
1.561.5910.2260.87211.7
1.541.5610.2620.83210.7
1.511.5410.3060.81110.2
ReflectionResolution: 1.51→50 Å / Num. obs: 142188 / % possible obs: 90.5 % / Redundancy: 11.5 % / Biso Wilson estimate: 12.53 Å2 / Rmerge(I) obs: 0.058 / Χ2: 1.689 / Net I/av σ(I): 51.882 / Net I/σ(I): 13 / Num. measured all: 1641294
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.51-1.5410.20.30661420.81179.2
1.54-1.5610.70.26262580.83280.9
1.56-1.5911.70.22661740.87279.4
1.59-1.6312.60.21562800.9380.8
1.63-1.6612.60.19863190.9481.5
1.66-1.712.40.1863670.97181.5
1.7-1.7412.20.15364241.02982.3
1.74-1.79120.13465881.0884.7
1.79-1.8411.60.11867621.19987.2
1.84-1.911.30.10569921.33689.5
1.9-1.9710.90.09672551.58692.8
1.97-2.0510.70.08974691.87195.5
2.05-2.1410.60.08176292.02197.2
2.14-2.2610.60.07176881.98398
2.26-2.410.80.06677632.02499.2
2.4-2.5811.10.06678622.23399.4
2.58-2.8411.40.05879092.33399.8
2.84-3.2511.80.05279292.63899.9
3.25-4.112.60.03980332.274100
4.1-5013.20.03783453.27199.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SOLVEphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8_1069)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.51→37.914 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1605 13405 5.02 %
Rwork0.117 253649 -
obs0.1192 267054 88.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.87 Å2 / Biso mean: 16.0903 Å2 / Biso min: 5.07 Å2
Refinement stepCycle: final / Resolution: 1.51→37.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8333 0 7 1427 9767
Biso mean--16.9 29.72 -
Num. residues----1097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128735
X-RAY DIFFRACTIONf_angle_d1.34311985
X-RAY DIFFRACTIONf_chiral_restr0.0891284
X-RAY DIFFRACTIONf_plane_restr0.0071617
X-RAY DIFFRACTIONf_dihedral_angle_d13.0213097
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.51-1.52430.22743620.13846878724072
1.5243-1.54220.16564040.10927538794277
1.5422-1.5610.17913940.11047534792880
1.561-1.58080.17824170.10077496791378
1.5808-1.60160.16094130.17569798279
1.6016-1.62350.17873500.09947668801879
1.6235-1.64670.16054020.09977619802179
1.6467-1.67130.16954310.09797645807680
1.6713-1.69740.15854170.10227639805680
1.6974-1.72520.15944060.10487696810280
1.7252-1.7550.16944110.10257719813080
1.755-1.78690.15064020.10467871827382
1.7869-1.82130.16454190.1087869828882
1.8213-1.85840.16944320.11328060849284
1.8584-1.89880.1784310.11148218864986
1.8988-1.9430.17514520.10928377882987
1.943-1.99160.1634520.11248579903190
1.9916-2.04540.1534680.11218751921992
2.0454-2.10560.16324640.11038976944093
2.1056-2.17360.14964770.10939061953895
2.1736-2.25130.15994980.11019263976196
2.2513-2.34140.16644840.11969345982998
2.3414-2.44790.1734950.12119478997398
2.4479-2.5770.1654970.1189427992499
2.577-2.73840.15445040.121955110055100
2.7384-2.94970.15795090.1299955510064100
2.9497-3.24640.15715090.1325958310092100
3.2464-3.71590.14655020.1181958110083100
3.7159-4.68020.14075010.1071960010101100
4.6802-37.92550.17385020.142795031000599

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