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- PDB-9r4m: Crystal structure of CtGH76 from Chaetomium thermophilum in compl... -

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Basic information

Entry
Database: PDB / ID: 9r4m
TitleCrystal structure of CtGH76 from Chaetomium thermophilum in complex with mannose products form
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 / FORMIC ACID / alpha-D-mannopyranose / Uncharacterized protein
Function and homology information
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)48,8607
Polymers48,0891
Non-polymers7716
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint7 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.524, 106.524, 127.109
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: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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.: 181 / 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

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: 1 Å
DetectorType: DECTRIS PILATUS4 X 2M / Detector: PIXEL / Date: Feb 24, 2023
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→43.36 Å / Num. obs: 60778 / % possible obs: 99.18 % / Redundancy: 19.9 % / Biso Wilson estimate: 46.99 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05114 / Rrim(I) all: 0.05252 / Net I/σ(I): 31.3
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 1.615 / Mean I/σ(I) obs: 1.94 / Num. unique obs: 5872 / CC1/2: 0.938 / % possible all: 96.74

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43.36 Å / SU ML: 0.2235 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1929 3017 5 %
Rwork0.1672 57310 -
obs0.1685 60327 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.64 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 51 181 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01942935
X-RAY DIFFRACTIONf_angle_d1.54394004
X-RAY DIFFRACTIONf_chiral_restr0.0976442
X-RAY DIFFRACTIONf_plane_restr0.0135519
X-RAY DIFFRACTIONf_dihedral_angle_d11.4127436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.40721280.38842456X-RAY DIFFRACTION94.34
1.98-2.020.3221350.32792572X-RAY DIFFRACTION98.98
2.02-2.050.28211340.29322564X-RAY DIFFRACTION98.4
2.05-2.090.28981320.26662531X-RAY DIFFRACTION98.3
2.09-2.130.26461350.24392576X-RAY DIFFRACTION98.62
2.13-2.170.2341350.22472547X-RAY DIFFRACTION98.35
2.17-2.220.21241350.19292586X-RAY DIFFRACTION99.13
2.22-2.270.22311380.18512583X-RAY DIFFRACTION98.87
2.27-2.330.21891360.1812558X-RAY DIFFRACTION99.26
2.33-2.390.21731360.17862581X-RAY DIFFRACTION99.49
2.39-2.460.2311370.1842606X-RAY DIFFRACTION99.67
2.46-2.540.23051370.19162602X-RAY DIFFRACTION99.49
2.54-2.630.23931380.19552612X-RAY DIFFRACTION99.67
2.63-2.740.24781360.21982604X-RAY DIFFRACTION99.85
2.74-2.860.27831380.20882621X-RAY DIFFRACTION99.78
2.86-3.010.21411390.20022618X-RAY DIFFRACTION99.78
3.01-3.20.21511380.18762629X-RAY DIFFRACTION99.82
3.2-3.450.20351400.18882660X-RAY DIFFRACTION99.96
3.45-3.790.18911400.14342639X-RAY DIFFRACTION100
3.8-4.340.11671400.11632663X-RAY DIFFRACTION99.96
4.34-5.470.15081420.12382693X-RAY DIFFRACTION100
5.47-43.360.18311480.15722809X-RAY DIFFRACTION99.83
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)
11.74957973992-0.165884078097-0.8524950694931.69120214354-0.02072577424474.937104457290.01456762950990.139297167729-0.142836744089-0.1693285488760.00277629354917-0.0429183453321.011112263840.744637091035-0.01305581207240.6800933166860.216055435773-0.008293000140130.520212489946-0.01060704428470.48366156370114.307864190153.681290610.062439603
21.58716630619-0.642042117103-0.5095819989841.772924606471.118764974134.17292900820.1049754803180.2336254715370.103789391664-0.114123027216-0.04230944852360.0810170641694-0.207557773282-0.3150088306084.00710807239E-50.5025315584410.0788544884729-0.01948371849910.4262429787890.02840003557420.5076972641262.1468503888968.717678693914.4764297986
32.22396914276-0.5183616488520.02445847597272.509839678910.3525032280155.114093496690.0984602610275-0.4164922363670.1947162373840.0477017368552-0.0180244044494-0.0606345503523-0.3950438786810.307695319025-2.12041200485E-50.518963512587-0.012093520384-0.001106628447120.406710256371-0.04922354126950.4360063028897.6826255564770.282309621530.1329696598
41.89186063423-1.309003574250.2773340138921.93495084130.7137706568293.794156630990.026562911658-0.3115516768230.2009768419170.2715864650020.0131675631802-0.4937202111090.1775560957961.349659138070.001062458866990.5782138819370.108063376716-0.05242043151150.899122133406-0.02514792203420.52561125136121.171573783162.88824719827.8480314065
51.599536420673.178806799761.053134872766.320916193142.096610969230.691918523678-0.1759865689550.154689216661-0.611709404925-0.5055045259380.835604263081-0.149745748761-1.2709154051-0.4987399876140.4889194559940.9724843813820.600456895626-0.01155565008141.242670188440.004351203277490.64089823633929.026636702942.058819034717.2354517737
60.391574960743-0.3305263860990.2632981861170.6620679314930.1855198272240.614167332650.0729056577394-0.0884245613914-0.4805499451270.3947857110240.0729523023125-0.4947447627820.8618710234621.537468029520.04081373981570.8126519840260.399365285152-0.06287536417080.9131946368020.0182877154380.64158895820921.467057157352.462678377324.2853055706
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 161 )78 - 1611 - 84
22chain 'A' and (resid 162 through 257 )162 - 25785 - 180
33chain 'A' and (resid 258 through 331 )258 - 331181 - 254
44chain 'A' and (resid 332 through 394 )332 - 394255 - 317
55chain 'A' and (resid 395 through 412 )395 - 412318 - 335
66chain 'A' and (resid 413 through 439 )413 - 439336 - 362

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