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- PDB-9r4s: Crystal structure of CtGH76 from Chaetomium thermophilum in compl... -

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Basic information

Entry
Database: PDB / ID: 9r4s
TitleCrystal structure of CtGH76 from Chaetomium thermophilum in complex with laminaribiose
ComponentsUncharacterized protein
KeywordsHYDROLASE / Glycoside Hydrolases / carbohydrate-binding protein
Function / homology: / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / beta-D-glucopyranose / FORMIC ACID / Uncharacterized protein
Function and homology information
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPo-Hsun, W. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 987 Germany
CitationJournal: Int J Mol Sci / Year: 2025
Title: Ct GH76, a Glycoside Hydrolase 76 from Chaetomium thermophilum , with Elongated Glycan-Binding Canyon.
Authors: Ruppenthal, S.R. / Po-Hsun, W. / Watad, M. / Rosner, C.J. / Vogt, M.S. / Friedrich, M. / Voigt, A.L. / Petz, A. / Gnau, P. / Essen, L.O.
History
DepositionMay 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2727
Polymers48,0891
Non-polymers1,1836
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint14 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.064, 107.064, 126.337
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 48089.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0025410 / Production host: Escherichia coli B (bacteria) / References: UniProt: G0S5Y9

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][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.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 3 types, 64 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.35 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.6 M sodium formate 10% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS4 X 2M / Detector: PIXEL / Date: Sep 21, 2020
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.2→46.36 Å / Num. obs: 42740 / % possible obs: 99.43 % / Redundancy: 2 % / Biso Wilson estimate: 48.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0229 / Rrim(I) all: 0.03238 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.2762 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 4217 / CC1/2: 0.929 / Rrim(I) all: 0.3906

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.36 Å / SU ML: 0.2371 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8473
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.205 2171 5.08 %
Rwork0.1824 40557 -
obs0.1836 42728 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.83 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 79 62 2953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512953
X-RAY DIFFRACTIONf_angle_d0.71354030
X-RAY DIFFRACTIONf_chiral_restr0.0423455
X-RAY DIFFRACTIONf_plane_restr0.0064514
X-RAY DIFFRACTIONf_dihedral_angle_d5.6396398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.36271330.30072488X-RAY DIFFRACTION99.47
2.25-2.30.32921280.27832518X-RAY DIFFRACTION99.51
2.3-2.360.2791140.27382508X-RAY DIFFRACTION99.32
2.36-2.420.28821190.26322503X-RAY DIFFRACTION99.28
2.42-2.490.25011360.2492544X-RAY DIFFRACTION99.37
2.49-2.570.26141070.23332515X-RAY DIFFRACTION99.43
2.57-2.670.28071350.23672504X-RAY DIFFRACTION99.21
2.67-2.770.26021160.22992542X-RAY DIFFRACTION99.77
2.77-2.90.251650.23122525X-RAY DIFFRACTION99.56
2.9-3.050.23961360.20522500X-RAY DIFFRACTION99.7
3.05-3.240.22761410.2072542X-RAY DIFFRACTION99.48
3.24-3.490.26291560.20552507X-RAY DIFFRACTION99.55
3.49-3.840.19011660.16712510X-RAY DIFFRACTION99.04
3.84-4.40.16031400.13762548X-RAY DIFFRACTION99.22
4.4-5.540.17241390.14322584X-RAY DIFFRACTION99.13
5.54-46.360.1531400.1582719X-RAY DIFFRACTION99.76
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)
10.3825422079980.1520088372260.1169783108960.0729263492208-0.006667097716530.2530736707940.1825622372260.163589400260.3969878344890.734739024699-0.161217126245-0.557945112547-0.9046767920681.17947635015-0.002442657122650.752949194451-0.3399062960790.01764696441811.02107140652-0.01425225593130.649620472024-32.745186194850.6463166704-25.791002325
22.002488398660.359231212549-0.4950436709871.41948556482-0.1538075675863.378442067910.003106983814830.129717074975-0.0900634756112-0.1745607743570.0356975795955-0.132015777685-0.07741384262460.454191296594-1.74571149944E-50.503312473915-0.01670868407120.01208900027630.660220603186-0.01746137883450.517944720776-46.376499054137.9219906336-33.5822459302
30.1993177578610.0808047584010.09151389529060.332784045847-0.05140950429740.475915248870.183484471064-0.165922454532-0.397938258139-0.09929011539530.0494750540680.04057450794891.00317248209-0.394606544076-0.0002372594923990.661606435286-0.0433991168011-0.003484006230360.6890201726250.02703930990670.624323417252-60.4915612525.7125828633-20.3556812557
40.5234567447970.239134969621-0.4366491324780.4120155327840.0422268084350.55018442224-0.07983413561590.2533434568820.0325410248294-0.04343223546060.1258019870670.286149716981-0.350784620727-0.93159924398-0.0001063823836160.4142473415820.09344618439570.009554543280140.7963885130380.03964274538780.559699057303-63.656481245240.1869023476-25.7621007401
52.273089110350.308575590742-0.250524305761.76735107358-0.2219393984094.623116715020.0800243805628-0.0379962211440.06359758973350.336966038085-0.04441668302510.0494715879444-0.5144554789630.08300526390788.31550608979E-80.5720809602250.03323369222070.02898151791150.581531146589-0.02931153565220.47385559902-53.917291873442.8336680571-12.9211776326
60.4756489270990.517250914011-0.013897070380.5759021369160.06282134075240.4685591084370.1658751925870.1210602481260.7839136025370.141330358774-0.1457850325130.145026956109-1.3546485470.2647080134117.01255118141E-61.30709675263-0.1629986105030.001694971086490.805702510865-0.06919620107750.823069104442-45.771356105258.7017154134-13.8994355042
70.5420948506-0.268869490263-0.3654321989640.2842327515760.09684989629550.2919134331250.387969215386-0.0939013906087-0.1844044875070.1095459739-0.682588613518-0.22145591636-0.213316847568-0.9909536032630.003724017125680.724351417439-0.382986727572-0.08072867871061.1583857570.03330368551760.734960077222-23.368341860747.8768087341-24.3852092426
80.7498868908260.623260642483-0.3164444448690.56082038156-0.1629769394710.3989979269590.0291163973655-0.2119907734080.04392650940830.2744140773680.0897877544677-0.183058909972-0.6542414716231.00685595538-0.0004776853505220.693721274568-0.212265827761-0.01338869377361.06574572636-0.05414917936060.658730198291-35.840269366645.9461620343-17.4294448304
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 78 through 96 )78 - 961 - 19
22chain 'A' and (resid 97 through 198 )97 - 19820 - 121
33chain 'A' and (resid 199 through 219 )199 - 219122 - 142
44chain 'A' and (resid 220 through 257 )220 - 257143 - 180
55chain 'A' and (resid 258 through 370 )258 - 370181 - 293
66chain 'A' and (resid 371 through 394 )371 - 394294 - 317
77chain 'A' and (resid 395 through 412 )395 - 412318 - 335
88chain 'A' and (resid 413 through 439 )413 - 439336 - 362

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