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- PDB-9r4u: Crystal structure of CtGH76 from Chaetomium thermophilum in compl... -

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Basic information

Entry
Database: PDB / ID: 9r4u
TitleCrystal structure of CtGH76 from Chaetomium thermophilum in complex with isomaltose
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: 1.96 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: CtGH76, 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

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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)48,8426
Polymers48,0891
Non-polymers7535
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint11 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.973, 106.973, 126.835
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, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+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.: 1 / 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, 151 molecules

#4: 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
#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.: 148 / 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: 4.36 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: 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: 1.96→49.28 Å / Num. obs: 60596 / % possible obs: 99.36 % / Redundancy: 2 % / Biso Wilson estimate: 44.54 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01035 / Rrim(I) all: 0.01463 / Net I/σ(I): 27.05
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.3166 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 5943 / CC1/2: 0.944 / Rrim(I) all: 0.4478

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→49.28 Å / SU ML: 0.2593 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.6289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 3028 5 %
Rwork0.1827 57568 -
obs0.1839 60596 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.93 Å2
Refinement stepCycle: LAST / Resolution: 1.96→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 50 148 3010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01782931
X-RAY DIFFRACTIONf_angle_d1.52493995
X-RAY DIFFRACTIONf_chiral_restr0.0903441
X-RAY DIFFRACTIONf_plane_restr0.0156517
X-RAY DIFFRACTIONf_dihedral_angle_d7.5093402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.990.50881320.45942530X-RAY DIFFRACTION97.83
1.99-2.020.38161390.38972621X-RAY DIFFRACTION99.42
2.02-2.050.4031350.34352563X-RAY DIFFRACTION98.72
2.05-2.090.28741360.2872548X-RAY DIFFRACTION98.5
2.09-2.130.27481350.24942583X-RAY DIFFRACTION98.8
2.13-2.180.21721340.21612557X-RAY DIFFRACTION98.68
2.18-2.220.22091360.19862579X-RAY DIFFRACTION98.91
2.22-2.270.231380.18582615X-RAY DIFFRACTION99.24
2.27-2.330.24261360.19622588X-RAY DIFFRACTION99.34
2.33-2.390.22721330.19732572X-RAY DIFFRACTION98.87
2.39-2.460.25391370.2042600X-RAY DIFFRACTION99.06
2.46-2.540.24491360.22282608X-RAY DIFFRACTION99.2
2.54-2.630.25971370.23292601X-RAY DIFFRACTION99.27
2.63-2.740.27511380.23792615X-RAY DIFFRACTION99.49
2.74-2.860.23751380.2242614X-RAY DIFFRACTION99.75
2.87-3.020.22581400.21152644X-RAY DIFFRACTION99.78
3.02-3.20.211390.20592638X-RAY DIFFRACTION99.78
3.21-3.450.23481400.19632657X-RAY DIFFRACTION99.96
3.45-3.80.20991380.16112633X-RAY DIFFRACTION100
3.8-4.350.151410.13072678X-RAY DIFFRACTION100
4.35-5.480.13041430.13782708X-RAY DIFFRACTION100
5.48-49.280.20081470.1642816X-RAY DIFFRACTION99.9
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)
11.44940447248-0.35220203765-0.401654316151.902384770440.1855039784295.32644272394-0.02097095418780.116452541559-0.102606248724-0.1184082249450.0441193144969-0.04668995551681.03990636750.833019623764-0.01450539378030.6852683763130.2045421596370.002532760038060.559166869013-0.01839989431910.4987990909414.595908112154.090798269110.0625672169
21.49626978305-0.539213355886-0.3804094855721.519472984960.7820510355054.715541806010.1183822024310.2155339571080.0196531837933-0.14017547535-0.06951741757410.0968332863959-0.262127921687-0.3560963870556.69255192601E-50.5116567168340.0542146192438-0.00422771991720.4465230979360.01660522199230.5290553254562.2868227783269.02141288314.2486311132
30.628330049821-0.07490836540140.9274955917892.533570639690.4124489669954.029998577790.0711525894965-0.2251896742720.1619694220810.03744847864070.01311445335150.0447353844081-0.330407334207-0.06469179731860.0001992507216660.522353465890.02108529924970.01779880506360.425092782845-0.02636885869510.481167892714.2022149445970.446663413328.6989287537
41.69575034393-0.6289246756080.1994943952581.165074038281.408344968273.692134217940.0785290577916-0.4651220867840.06047539393760.287838928828-0.0217273622598-0.08890791525520.2690414104261.112008613188.91216888543E-50.5857568739770.0458868736861-0.01890075613950.762329001275-0.04154981601260.50210008237816.127110215864.434744828629.7553784967
51.5639494939-0.457778009698-0.5129423542410.1025934645650.08994206135442.73139860881-0.0332108582891-0.7051121159130.4485711803370.1543652515060.369585951069-1.04589015975-0.4077822505142.338211447190.1405499232370.663581031316-0.00851457012192-0.06100373209271.55895912109-0.09693257168710.70734542997728.218786767267.781506117427.964377202
61.867470392993.207907500111.130486932945.811838474861.993612646130.625511098991-0.3237544635960.130883812779-0.662171678751-0.4582451478181.10372698165-0.41598281221-1.19077514191-0.4069774041470.4465479168311.032931942890.615571698681-0.06647039691291.373115453460.0614870772180.65556673168629.183539927542.597329879617.443490275
70.689647561903-0.3902512584760.3862287734320.7990791209990.4335007726390.9851294918850.00574979964523-0.37259210248-0.3908131014230.1612464876590.0214865968946-0.2934641150381.156009738651.796162202170.05141426005970.8380485019560.455868369872-0.04931383464570.9834009724050.02423454114660.60520131013721.587726723852.669768490424.6630403765
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 308 )258 - 308181 - 231
44chain 'A' and (resid 309 through 369 )309 - 369232 - 292
55chain 'A' and (resid 370 through 394 )370 - 394293 - 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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