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- PDB-9r4q: Crystal structure of CtGH76 from Chaetomium thermophilum in compl... -

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Basic information

Entry
Database: PDB / ID: 9r4q
TitleCrystal structure of CtGH76 from Chaetomium thermophilum in complex with alpha-1,3-1,6-mannotriose
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 / FORMIC ACID / Uncharacterized protein
Function and homology information
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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)48,8245
Polymers48,0891
Non-polymers7354
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint6 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.099, 107.099, 126.544
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 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
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a6-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 54 / 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: 4.36 Å3/Da / Density % sol: 71.77 %
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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 22, 2023
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.7→43.54 Å / Num. obs: 23467 / % possible obs: 99.52 % / Redundancy: 20.4 % / Biso Wilson estimate: 60.35 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 15.45
Reflection shellResolution: 2.7→2.796 Å / Mean I/σ(I) obs: 1.48 / Num. unique obs: 2307 / CC1/2: 0.872

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→43.54 Å / SU ML: 0.4357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.133
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 1196 5.1 %
Rwork0.1973 22271 -
obs0.1991 23467 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.96 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 49 54 2915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052929
X-RAY DIFFRACTIONf_angle_d0.66223992
X-RAY DIFFRACTIONf_chiral_restr0.0413441
X-RAY DIFFRACTIONf_plane_restr0.0058517
X-RAY DIFFRACTIONf_dihedral_angle_d13.7316433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.810.50311330.39682447X-RAY DIFFRACTION99.38
2.81-2.940.35161350.31692376X-RAY DIFFRACTION99.13
2.94-3.090.33411170.27372465X-RAY DIFFRACTION99.46
3.09-3.280.31051310.26782426X-RAY DIFFRACTION99.69
3.28-3.540.28991350.23822466X-RAY DIFFRACTION99.77
3.54-3.890.22531460.18682453X-RAY DIFFRACTION99.92
3.89-4.460.18261140.14812517X-RAY DIFFRACTION100
4.46-5.610.15591570.15352492X-RAY DIFFRACTION100
5.61-43.540.20131280.16452629X-RAY DIFFRACTION99.75
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)
11.83974346023-1.718422284420.03883109498791.94640225752-0.4878667528242.985158174620.1312442347620.0575512775756-0.300258345082-0.330040566733-0.113899677988-0.2064940929710.9152185060381.19760758454-0.0007077771845290.7965165606610.2280970090260.01542992252410.765425594127-0.009686242915760.62407662705319.081076264253.303449496713.7634714642
22.09238009576-0.7270314287070.1157405785121.603197362870.237062849223.651078327270.083957900150.304998647026-0.0335956189792-0.0783228756615-0.009196409375360.0661112875330.4213330018450.185678002240.0002051824982410.626174293760.0179793485989-0.01130839153710.585982190426-0.01478683184260.5877128522557.1685021426760.59921769416.8706463809
32.25812281631-1.171706299290.03845902423931.177445407431.152234361762.533393838380.1246656127950.2699783828530.275076600005-0.0402155995651-0.03735961188470.27328132694-0.556980809511-0.6581309142930.0008354230881480.5956705858730.0733991053624-0.009226895118830.5162763614340.005339759593590.614026190935-0.36613397094271.857964548718.1437097263
41.30205546471-0.4214460572010.7022349516912.892329609860.5617845427383.138047935590.00846576992178-0.326158057893-0.01853523324280.0405077910873-0.0801882035464-0.0479575315505-0.240729138732-0.1007989871452.42063982426E-50.6005872131780.0378715676078-0.004896898656670.491709186303-0.04063881220640.5732356965853.9480764020570.409463180328.751124671
51.41987194690.375298724169-0.2931403932930.8170286833830.8445739367211.27951026642-0.087272891649-0.599010007560.4291902263990.1943616954170.00887874670349-0.340235283303-0.5309197415921.02728211933-0.001604421169220.758885629762-0.123859935281-0.01794405418660.906808958142-0.1035831308610.68633152699116.325558065472.851283045532.4377709404
62.76345359602-0.764531845709-0.163611825431.843301433041.059137932524.20788313650.0759401897103-0.446364731228-0.00597821068655-0.0533046222762-0.147248001876-0.3600592030790.2613856915781.56317967895-0.000960540722660.6409595103030.0668055814379-0.0413653425441.08358918676-0.0009266396450610.61218385940321.803431199762.655214555427.7104198567
70.466361909829-0.526856229624-0.4912531774230.8489984882550.7003666391390.54455069808-0.1248422205150.053928228066-0.265965533460.3499206411960.140531044035-0.06964066326770.3034419893420.357805531936-0.0004072083768380.8915756171640.318707584716-0.02625613119390.9549331240270.01595531268020.7483416477524.238169332148.917656505721.5419967612
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 127 )78 - 1271 - 50
22chain 'A' and (resid 128 through 198 )128 - 19851 - 121
33chain 'A' and (resid 199 through 257 )199 - 257122 - 180
44chain 'A' and (resid 258 through 307 )258 - 307181 - 230
55chain 'A' and (resid 308 through 331 )308 - 331231 - 254
66chain 'A' and (resid 332 through 398 )332 - 398255 - 321
77chain 'A' and (resid 399 through 439 )399 - 439322 - 362

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