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- PDB-6p2o: Crystal structure of Streptomyces rapamycinicus GH74 in complex w... -

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Basic information

Entry
Database: PDB / ID: 6p2o
TitleCrystal structure of Streptomyces rapamycinicus GH74 in complex with xyloglucan fragments XLLG and XXXG
ComponentsXyloglucanase
KeywordsHYDROLASE / glycosyl hydrolase / GH74 / xyloglucanase / 7-fold beta-propeller
Function / homologyYVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta / Xyloglucanase
Function and homology information
Biological speciesStreptomyces rapamycinicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsStogios, P.J. / Skarina, T. / Arnal, G. / Brumer, H. / Savchenko, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Industrial Biocatalysis Network Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74.
Authors: Arnal, G. / Stogios, P.J. / Asohan, J. / Attia, M.A. / Skarina, T. / Viborg, A.H. / Henrissat, B. / Savchenko, A. / Brumer, H.
History
DepositionMay 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 8, 2020Group: 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 / 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_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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: Xyloglucanase
B: Xyloglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,60128
Polymers155,0402
Non-polymers6,56226
Water46,1182560
1
A: Xyloglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,82914
Polymers77,5201
Non-polymers3,30913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xyloglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,77214
Polymers77,5201
Non-polymers3,25213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.996, 112.788, 222.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Xyloglucanase


Mass: 77519.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rapamycinicus (strain ATCC 29253 / DSM 41530 / NRRL 5491 / AYB-994) (bacteria)
Strain: ATCC 29253 / DSM 41530 / NRRL 5491 / AYB-994 / Gene: D3C57_132765 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A0NH71

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1387.204 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-1-1-1-2-2-3-2-3/a4-b1_b4-c1_b6-h1_c4-d1_c6-f1_d6-e1_f2-g1_h2-i1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-2-2-2/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 2582 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2560 / 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: 3.77 Å3/Da / Density % sol: 67.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 0.1 M sodium chloride, 0.1 M Hepes pH 7.5, xyloglucan mixture

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.88→25 Å / Num. obs: 172049 / % possible obs: 89.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.043 / Net I/σ(I): 12.2
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.954 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8554 / CC1/2: 0.541 / Rpim(I) all: 0.565 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX(1.15_3448: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JWZ

5jwz


Resolution: 1.88→24.822 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 3304 1.27 %RANDOM
Rwork0.1481 ---
obs0.1486 156964 70.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→24.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10962 0 421 2560 13943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311720
X-RAY DIFFRACTIONf_angle_d1.13316022
X-RAY DIFFRACTIONf_dihedral_angle_d4.2358756
X-RAY DIFFRACTIONf_chiral_restr0.0711757
X-RAY DIFFRACTIONf_plane_restr0.0082023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90680.3041510.28873633X-RAY DIFFRACTION24
1.9068-1.93530.3357610.23754610X-RAY DIFFRACTION31
1.9353-1.96550.2759730.22155768X-RAY DIFFRACTION38
1.9655-1.99770.2404920.20516952X-RAY DIFFRACTION46
1.9977-2.03220.23681030.19187948X-RAY DIFFRACTION52
2.0322-2.06910.22191130.19238827X-RAY DIFFRACTION58
2.0691-2.10890.18261200.19159578X-RAY DIFFRACTION63
2.1089-2.15190.17571330.190710309X-RAY DIFFRACTION68
2.1519-2.19870.21831350.18610694X-RAY DIFFRACTION71
2.1987-2.24980.24141460.185411260X-RAY DIFFRACTION74
2.2498-2.3060.26861530.197711935X-RAY DIFFRACTION79
2.306-2.36830.19781580.176912145X-RAY DIFFRACTION80
2.3683-2.43790.23981630.17212529X-RAY DIFFRACTION83
2.4379-2.51660.22741550.165312534X-RAY DIFFRACTION83
2.5166-2.60640.20791610.165912447X-RAY DIFFRACTION82
2.6064-2.71060.22261610.162312347X-RAY DIFFRACTION82
2.7106-2.83380.21511570.160412311X-RAY DIFFRACTION81
2.8338-2.9830.19571550.151412308X-RAY DIFFRACTION81
2.983-3.16960.17181520.143912395X-RAY DIFFRACTION82
3.1696-3.41370.19421700.130112811X-RAY DIFFRACTION85
3.4137-3.75620.11981660.111313238X-RAY DIFFRACTION87
3.7562-4.29730.11521760.105113546X-RAY DIFFRACTION90
4.2973-5.40490.11971770.103413598X-RAY DIFFRACTION90
5.4049-24.82370.18711730.153513449X-RAY DIFFRACTION89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.25311.17550.64313.70191.46982.11010.0417-0.02250.09620.1572-0.13490.3529-0.0842-0.25010.09630.17360.00330.06470.15840.01560.1342-24.140764.3615-39.4656
20.79540.6030.41942.11090.39360.873-0.0181-0.00340.02960.0720.032-0.0516-0.06410.0073-0.01190.1523-0.00760.00570.0991-0.00170.1167-5.979772.5129-43.2045
31.19121.15040.42041.2601-0.02041.50250.2329-0.20320.04240.6582-0.166-0.22050.08170.0174-0.06210.4158-0.049-0.08250.1848-0.01660.1722-2.139770.548-23.5563
40.60450.06250.23910.22020.36960.69790.2181-0.2557-0.14680.878-0.09-0.01160.1964-0.1306-0.09920.6898-0.1151-0.02260.25310.00350.2168-12.290357.2015-17.6125
50.8260.35910.65931.20891.07191.7680.146-0.2245-0.00790.381-0.12860.1309-0.1163-0.2354-0.01880.3432-0.05490.08350.1963-0.0060.1828-21.005359.851-28.412
61.4532-1.5083-0.75083.59130.66362.1186-0.0322-0.1641-0.04930.29410.07130.09430.12140.1019-0.04130.1538-0.05270.0070.17480.03050.1263-19.790832.5013-39.1839
75.1298-0.66160.14073.07740.50092.29910.02940.0265-0.1687-0.1939-0.05590.12920.3191-0.08240.02260.1821-0.0334-0.03670.12170.0160.0903-18.481927.7623-57.5489
82.2997-0.7052-0.25471.71330.12082.3232-0.03240.1267-0.0131-0.343-0.04380.29660.0198-0.21890.05710.1897-0.0488-0.06430.16050.01850.1476-25.015938.2846-64.0968
92.10350.75860.37352.05980.43163.1215-0.0270.06690.0566-0.128-0.02080.3936-0.1906-0.3320.0410.1256-0.001-0.04260.15710.01480.1953-29.449.0115-55.8411
100.5313-0.01930.2090.50730.15840.70230.0031-0.02280.0039-0.04320.01740.03580.0477-0.0018-0.02180.0744-0.01110.00830.1073-0.01670.09971.76447.865-19.3126
111.71940.98810.39551.46730.24180.7138-0.21220.15990.3184-0.21720.10680.1965-0.17080.0790.08860.1184-0.0276-0.05750.162-0.00680.167418.872436.8977-6.7498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 46 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 301 )
3X-RAY DIFFRACTION3chain 'A' and (resid 302 through 356 )
4X-RAY DIFFRACTION4chain 'A' and (resid 357 through 413 )
5X-RAY DIFFRACTION5chain 'A' and (resid 414 through 482 )
6X-RAY DIFFRACTION6chain 'A' and (resid 483 through 596 )
7X-RAY DIFFRACTION7chain 'A' and (resid 597 through 658 )
8X-RAY DIFFRACTION8chain 'A' and (resid 659 through 706 )
9X-RAY DIFFRACTION9chain 'A' and (resid 707 through 772 )
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 526 )
11X-RAY DIFFRACTION11chain 'B' and (resid 527 through 772 )

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