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- PDB-9r4k: Crystal structure of CtGH76 from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 9r4k
TitleCrystal structure of CtGH76 from Chaetomium thermophilum
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 / Uncharacterized protein
Function and homology information
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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)48,5267
Polymers48,0891
Non-polymers4376
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-6 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.787, 106.787, 126.898
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.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 4.34 Å3/Da / Density % sol: 71.68 %
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: Mar 28, 2019
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→49.21 Å / Num. obs: 55077 / % possible obs: 99.35 % / Redundancy: 2 % / Biso Wilson estimate: 39.76 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01495 / Rrim(I) all: 0.02115 / Net I/σ(I): 29.64
Reflection shellResolution: 2.02→2.09 Å / Rmerge(I) obs: 0.2827 / Mean I/σ(I) obs: 2.73 / Num. unique obs: 5395 / CC1/2: 0.959 / CC star: 0.989 / Rrim(I) all: 0.3998

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→49.21 Å / SU ML: 0.2681 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 2724 4.97 %
Rwork0.1928 52059 -
obs0.1938 54783 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.69 Å2
Refinement stepCycle: LAST / Resolution: 2.02→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 28 206 3040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022915
X-RAY DIFFRACTIONf_angle_d0.45173972
X-RAY DIFFRACTIONf_chiral_restr0.0358428
X-RAY DIFFRACTIONf_plane_restr0.0029520
X-RAY DIFFRACTIONf_dihedral_angle_d5.4944409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.060.37171690.39142621X-RAY DIFFRACTION97.72
2.06-2.10.34221670.34272679X-RAY DIFFRACTION98.55
2.1-2.140.32441180.30722674X-RAY DIFFRACTION98.66
2.14-2.190.28541820.27512645X-RAY DIFFRACTION98.19
2.19-2.240.2811770.25042671X-RAY DIFFRACTION98.96
2.24-2.290.28231390.24052723X-RAY DIFFRACTION99.34
2.29-2.360.25361410.23122701X-RAY DIFFRACTION99.37
2.36-2.430.26511290.22592710X-RAY DIFFRACTION99.37
2.43-2.50.24581210.23242768X-RAY DIFFRACTION99.14
2.5-2.590.28861420.2382711X-RAY DIFFRACTION99.23
2.59-2.70.2721170.23812750X-RAY DIFFRACTION99.48
2.7-2.820.21241220.23292784X-RAY DIFFRACTION99.9
2.82-2.970.26051280.22562758X-RAY DIFFRACTION99.86
2.97-3.150.22791330.21332760X-RAY DIFFRACTION99.86
3.16-3.40.25171550.20062762X-RAY DIFFRACTION99.9
3.4-3.740.19421500.17082765X-RAY DIFFRACTION100
3.74-4.280.1431410.14012809X-RAY DIFFRACTION100
4.28-5.390.15011300.14462829X-RAY DIFFRACTION100
5.39-49.210.18241630.16352939X-RAY DIFFRACTION99.94
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)
11.36083986105-0.560230022854-0.08363120923091.2454048237-0.5000048475192.10103741426-0.103332875178-0.114666431449-0.0657682595105-0.1844170475270.0165553431876-0.1157571850871.041443902781.44639290547-0.03821998628420.723514954530.3263580763180.01336023020490.6802137781140.004308615822680.45400612408518.980673805253.179029624213.5690184732
21.01285028057-0.7455704843830.1766912561291.515686729620.077184522894.079612028460.03139464416610.2465789852240.0235369566691-0.164624971847-0.005738808075040.05551613462730.3806293656780.1344533075.11655043107E-50.4920143322460.049801966301-0.02464090573090.420992953037-0.01366574258470.4077565480286.9875201057860.61572366286.86623856386
31.84626134351-0.472074400577-0.6413232832291.070697047861.346515256672.587104180790.1396732749320.2365797662010.193587525686-0.214359285696-0.009827602555210.262387985083-0.410564341778-0.5935825685940.0001502069959480.4952661760990.08453632301860.002544119275390.3986423839230.02086695016780.460845648677-0.49919546786671.675130476218.3336648837
41.46789957946-0.555847006377-0.01060102442962.20394342360.182635670415.075508091680.0649469485531-0.4201674393730.1685391577120.0790116820932-0.0368111929633-0.0721019138453-0.4071215529730.413671236134-0.0003728461248690.477691159819-0.00887745163844-0.0008269255776440.398261995547-0.05287734941540.3869449224267.6139885335270.747312835530.0049412533
52.18966105182-0.964235310376-0.3680575293791.630659785420.8189415004033.70939790887-0.0215144719337-0.4254425670060.1784763264210.185375552320.071980992383-0.360663598120.2997282043261.596909707950.008257024916070.5209307805960.106543708546-0.06194311244260.975584189566-0.03520599531260.43726899112421.267618494363.347903639527.8723684395
64.407903638592.030061522010.06644533215697.045850285211.614320388610.400880450476-0.0473471711921-0.115284133959-0.50683445437-0.3421079817550.542987532124-0.290719054475-0.95915001863-0.9147132662961.116282251710.8649989384590.642066847409-0.04219180147431.21463908110.1328219154770.52521977620829.239742054942.684083805117.4399989576
70.362172395844-0.1747152833590.9662804126181.256707857170.02370215564782.770004872860.0309817382022-0.461037457812-0.4952822732050.394109620040.102800898362-0.5537800080620.9876359135561.649863457640.5649343114760.7154759887280.489984583483-0.05663411500570.9206627878350.03744887165770.51778418183321.58821262753.034283293424.3905246668
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 331 )258 - 331181 - 254
55chain 'A' and (resid 332 through 394 )332 - 394255 - 317
66chain 'A' and (resid 395 through 412 )395 - 412318 - 335
77chain 'A' and (resid 413 through 439 )413 - 439336 - 362

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