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- PDB-5h4r: the complex of Glycoside Hydrolase 5 Lichenase from Caldicellulos... -

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Basic information

Entry
Database: PDB / ID: 5h4r
Titlethe complex of Glycoside Hydrolase 5 Lichenase from Caldicellulosiruptor sp. F32 E188Q mutant and cellotetraose
ComponentsBeta-1,3-1,4-glucanaseEndo-1,3(4)-b-glucanase
KeywordsHYDROLASE / Glycoside Hydrolase 5 Lichenase
Function / homology
Function and homology information


organic substance metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellotetraose / Beta-1,3-1,4-glucanase
Similarity search - Component
Biological speciesCaldicellulosiruptor sp. F32 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.70310440144 Å
AuthorsDong, S. / Zhou, H. / Liu, X. / Wang, X. / Feng, Y.
CitationJournal: Biochem. J. / Year: 2017
Title: Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32
Authors: Meng, D.D. / Liu, X. / Dong, S. / Wang, Y.F. / Ma, X.Q. / Zhou, H. / Wang, X. / Yao, L.S. / Feng, Y. / Li, F.L.
History
DepositionNov 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.type / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6413
Polymers45,8821
Non-polymers7592
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-6 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.581, 76.315, 95.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Beta-1,3-1,4-glucanase / Endo-1,3(4)-b-glucanase / Glycoside hydrolase F32EG5


Mass: 45882.055 Da / Num. of mol.: 1 / Mutation: E188Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor sp. F32 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: R9RX81
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 8.5 / Details: 0.2 M ammonium sulfate, 0.1 M Tris, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.703→28.4 Å / Num. obs: 49925 / % possible obs: 98.31 % / Redundancy: 5 % / Biso Wilson estimate: 13.3259821509 Å2 / Net I/σ(I): 33.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimlessdata scaling
PHASERdata processing
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X0V

4x0v


Resolution: 1.70310440144→28.3996626024 Å / SU ML: 0.122328358275 / Cross valid method: FREE R-VALUE / σ(F): 1.52833935836 / Phase error: 14.1704917007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.169842103488 2539 5.08583218156 %
Rwork0.14126438051 47384 -
obs0.142735000316 49923 98.304584121 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.1023835659 Å2
Refinement stepCycle: LAST / Resolution: 1.70310440144→28.3996626024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 51 443 3561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008541558747183228
X-RAY DIFFRACTIONf_angle_d0.9915621084624385
X-RAY DIFFRACTIONf_chiral_restr0.0619506266646470
X-RAY DIFFRACTIONf_plane_restr0.00683411717955555
X-RAY DIFFRACTIONf_dihedral_angle_d8.868109520821894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7031-1.73590.1844954645921150.1567209196112307X-RAY DIFFRACTION86.9034804449
1.7359-1.77130.1952459713171450.1504086711212536X-RAY DIFFRACTION97.1376811594
1.7713-1.80980.1409051507741290.1319829041812634X-RAY DIFFRACTION99.0322580645
1.8098-1.85190.1661789535271510.1324740091652614X-RAY DIFFRACTION99.4246673858
1.8519-1.89820.157214411241550.1281511605572630X-RAY DIFFRACTION99.2162451015
1.8982-1.94950.1590789112261330.1318868395642611X-RAY DIFFRACTION99.1687748464
1.9495-2.00680.1731062259711400.1328558895912641X-RAY DIFFRACTION99.0737442109
2.0068-2.07160.1638556302021480.1246978550622625X-RAY DIFFRACTION99.5333811917
2.0716-2.14560.162510096071370.1243758670082655X-RAY DIFFRACTION99.359430605
2.1456-2.23150.1645912913611470.1229132613982625X-RAY DIFFRACTION99.3904625314
2.2315-2.3330.1541843176761280.1260658450132675X-RAY DIFFRACTION99.3619283942
2.333-2.45590.1579105957311220.1334193881782675X-RAY DIFFRACTION99.6437477734
2.4559-2.60970.1747237421841450.1356468084282662X-RAY DIFFRACTION99.3980169972
2.6097-2.81110.1674742692971350.1420639052932677X-RAY DIFFRACTION99.3990809473
2.8111-3.09360.1713259207541450.144406030922674X-RAY DIFFRACTION99.3655269651
3.0936-3.54060.2052726431251490.1505355282832688X-RAY DIFFRACTION99.1958041958
3.5406-4.4580.158678844251470.1400242604342687X-RAY DIFFRACTION97.7915804003
4.458-28.40360.1739626991341680.1780130125772768X-RAY DIFFRACTION97.1542025149
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)
11.38017620244-0.332887821317-0.01093972792471.41860484815-0.374932922541.00782599001-0.01096221857750.07059698012740.00112708395923-0.0772758488714-0.000208680279087-0.01614878014460.098047405095-0.006278750031460.005025582044670.0552804639175-0.0263194113352-0.01897959163240.045029819221-0.007056096221790.081526792893931.719457087643.63225992528.33345618651
22.39198591819-0.751644946229-1.94578242162.895525708012.890253340915.7684547022-0.02287393016210.0513287409178-0.110308317116-0.0406277608186-0.0937559722910.2730520452870.0707606101083-0.3206448849450.1371845400380.0794378515123-0.00522289627651-0.0150999007220.08987058451630.04558899238510.14044938916317.151939852741.795029882715.4615356268
31.171365587910.1872758607190.06615460710351.255478249190.1044148993161.838523527040.0144255068173-0.146022963055-0.07337461674220.1260493120710.02578071458040.08445371090880.0999229083426-0.0891038892416-0.0363764772750.06773250416090.0184278848780.00106805316680.08184405079610.02558460168440.095122307593927.363514408240.339093221823.4776253606
45.319707698364.510831482551.961483693874.1148165592.048960894452.198015212350.106523737374-0.3791353905040.09362590146110.30051113978-0.1637805938930.0280892249037-0.00552609838218-0.06771457794910.05596449196020.1104668344690.0183719704527-0.00786185337720.1297958225770.0250317537080.077585683650436.366948514541.004666945433.4324153595
51.263626504880.6749449110690.3676753602922.711588083810.5586451636211.04518649897-0.00270426123849-0.07842521938260.00579875698827-0.111481441250.00490636131876-0.261946020987-0.0686949393580.02992946220170.004011800908680.05388221162310.01634356326690.009917137055440.1014924313130.01058867158940.088228399278538.663904234246.836452642421.9796410325
63.614521915563.947974091150.556605894314.379795525160.8260939456721.339409200410.0741274713823-0.196747057615-0.01161393410630.278944528239-0.153470856953-0.20360174119-0.04150299754080.01493052511840.06988773094140.09121704790860.0217241588595-0.01977653952810.1094496553580.01770718311460.095231861318845.607979852643.650204016928.1408078812
71.295245329051.5914652108-0.1705769776635.23749963728-0.4685304433590.8224866687430.00511917879294-0.0840067917927-0.1160186710760.0567987542617-0.0501147738854-0.2893010286220.06814190813420.1448114901040.04238973102240.06917705577750.0166602684835-0.001429506170460.09630551350480.008150926210270.072802262395945.052529479941.088265099319.711532772
82.32351661715-2.702914642481.081799697017.73782061051-2.87960151162.44646398615-0.0401295675173-0.0168295498168-0.1702388183250.1276564496930.00316406373552-0.03170524969490.08329572129520.07851038085950.04096278906230.0435735744726-0.01222112151810.01042934168460.0894209727333-0.0131834059670.062557894437641.017770698344.398248560712.5264830165
91.73449520943-0.451735739316-0.01332959300461.02332825497-0.2827711054790.966092634423-0.01566521437220.05307909339260.0709051541415-0.0542800131915-0.013987309324-0.0587171587323-0.02978053939230.02718029962320.0214994608790.0626728303233-0.0103999610138-0.003498570336180.053389045236-0.009242604757620.050400050484535.662935429153.25598361074.05161860013
103.87059638710.506146118613-0.6602783387731.9131672992-0.1169514063843.81373174832-0.1310994027140.113886233862-0.0456790111673-0.1033244409210.08002220391520.1241532715510.155187794255-0.1892947865810.04394428581470.0801057172854-0.0167929937983-0.03345233663780.04888806367320.01288144248750.073132085551422.983213219646.02692048521.11940957829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 152 )
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 173 )
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 204 )
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 228 )
7X-RAY DIFFRACTION7chain 'A' and (resid 229 through 260 )
8X-RAY DIFFRACTION8chain 'A' and (resid 261 through 280 )
9X-RAY DIFFRACTION9chain 'A' and (resid 281 through 371 )
10X-RAY DIFFRACTION10chain 'A' and (resid 372 through 396 )

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