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- PDB-9r4t: Crystal structure of CtGH76 from Chaetomium thermophilum in compl... -

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Basic information

Entry
Database: PDB / ID: 9r4t
TitleCrystal structure of CtGH76 from Chaetomium thermophilum in complex with glucose
ComponentsChains: A
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 / Uncharacterized protein
Function and homology information
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Chains: A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9067
Polymers48,0891
Non-polymers8176
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint7 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.237, 107.237, 127.024
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

#1: Protein Chains: A


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 3 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
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: 4.38 Å3/Da / Density % sol: 71.95 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / 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: 2.3→49.4 Å / Num. obs: 37894 / % possible obs: 99.6 % / Redundancy: 10.7 % / Biso Wilson estimate: 48.93 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1065 / Rrim(I) all: 0.1119 / Net I/σ(I): 11.63
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.8632 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 3755 / CC1/2: 0.938 / Rrim(I) all: 0.907

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.4 Å / SU ML: 0.2177 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2084 1902 5.02 %
Rwork0.189 35981 -
obs0.19 37883 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 54 94 2960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232934
X-RAY DIFFRACTIONf_angle_d0.49444000
X-RAY DIFFRACTIONf_chiral_restr0.0361441
X-RAY DIFFRACTIONf_plane_restr0.0035517
X-RAY DIFFRACTIONf_dihedral_angle_d5.5741404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.34351280.30832522X-RAY DIFFRACTION99.33
2.36-2.420.30031270.28892560X-RAY DIFFRACTION99.48
2.42-2.490.32371360.26932512X-RAY DIFFRACTION98.99
2.49-2.570.30671370.26122525X-RAY DIFFRACTION99.37
2.57-2.660.23771260.23522524X-RAY DIFFRACTION99.29
2.67-2.770.2951470.22652565X-RAY DIFFRACTION99.56
2.77-2.90.25281680.22712504X-RAY DIFFRACTION99.59
2.9-3.050.24281420.20952538X-RAY DIFFRACTION99.52
3.05-3.240.2276940.22442616X-RAY DIFFRACTION99.74
3.24-3.490.24141210.20632578X-RAY DIFFRACTION99.93
3.49-3.840.19681570.1762578X-RAY DIFFRACTION99.82
3.84-4.40.17591310.14652599X-RAY DIFFRACTION99.96
4.4-5.540.16731510.15262622X-RAY DIFFRACTION100
5.54-49.40.17061370.16972738X-RAY DIFFRACTION99.79
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)
11.812268123190.528015161101-0.3085468105091.34729466852-0.1109637607525.308668780450.076654053786-0.03724020138540.08102066155690.2455506259820.01981691928890.105009282541-0.611069508664-0.06886662494590.0003575004247520.5607845106350.03870767742760.03008961439110.568542131437-0.009782010408960.546375298343-55.269281282442.4708973241-16.5855402165
20.6381238468260.438625763598-0.299465273480.432757985052-0.1867965153920.1314529014420.149520608833-0.393181103304-0.08833685799870.0495539638576-0.0774025221888-0.360671356668-0.4413461079570.427169323192-0.0002058198159940.694374463437-0.29544412081-0.03203081939251.22397908203-0.01448717833860.698582746335-30.224351042546.2943381859-20.7378498648
32.034416096210.486378982823-0.1352863600611.618345940020.04047781390653.843652855880.03780454001460.0851388485030.0375335969017-0.135747630746-0.0138213952036-0.0544852271325-0.1977513486770.6744443667154.54536321852E-50.540997378741-0.03129396118710.01401407878810.734655895003-0.01627921288460.555555605351-44.413165147939.3518545351-32.8076293929
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 199 through 394 )199 - 394122 - 317
22chain 'A' and (resid 395 through 439 )395 - 439318 - 362
33chain 'A' and (resid 78 through 198 )78 - 1981 - 121

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