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- PDB-9r4o: Crystal structure of inactive (D163N) variant CtGH76 from Chaetom... -

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Basic information

Entry
Database: PDB / ID: 9r4o
TitleCrystal structure of inactive (D163N) variant CtGH76 from Chaetomium thermophilum in complex with alpha-1,6-mannobiose
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 / alpha-D-mannopyranose / Uncharacterized protein
Function and homology information
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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)48,7034
Polymers48,0881
Non-polymers6153
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint10 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.024, 107.024, 127.541
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: 48088.094 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-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M sodium/potassium tartrate 0.2 M lithium sulfate 0.1 M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS4 X 2M / Detector: PIXEL / Date: Feb 23, 2021
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.13→49.34 Å / Num. obs: 47326 / % possible obs: 99.08 % / Redundancy: 2 % / Biso Wilson estimate: 53.47 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01738 / Rrim(I) all: 0.02458 / Net I/σ(I): 16.84
Reflection shellResolution: 2.13→2.206 Å / Rmerge(I) obs: 0.5351 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 4615 / CC1/2: 0.896 / CC star: 0.972 / Rrim(I) all: 0.7567 / % possible all: 98.25

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→49.34 Å / SU ML: 0.3348 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.3344
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2259 2367 5 %
Rwork0.2072 44959 -
obs0.2081 47326 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.6 Å2
Refinement stepCycle: LAST / Resolution: 2.13→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 41 63 2916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232924
X-RAY DIFFRACTIONf_angle_d0.49363989
X-RAY DIFFRACTIONf_chiral_restr0.0352441
X-RAY DIFFRACTIONf_plane_restr0.0065517
X-RAY DIFFRACTIONf_dihedral_angle_d9.7522432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.170.50661300.48162496X-RAY DIFFRACTION95.63
2.17-2.220.49561380.4452625X-RAY DIFFRACTION99
2.22-2.270.42651390.41242616X-RAY DIFFRACTION98.78
2.27-2.330.42351380.3712604X-RAY DIFFRACTION99.02
2.33-2.390.31961370.32792610X-RAY DIFFRACTION98.49
2.39-2.460.33831370.3022607X-RAY DIFFRACTION98.74
2.46-2.540.31461400.29092627X-RAY DIFFRACTION98.75
2.54-2.630.32181350.25812603X-RAY DIFFRACTION98.56
2.63-2.740.31291390.27732637X-RAY DIFFRACTION99.07
2.74-2.860.30121400.27082647X-RAY DIFFRACTION99.18
2.86-3.010.26751370.24622621X-RAY DIFFRACTION99.07
3.01-3.20.2511410.23892662X-RAY DIFFRACTION99.05
3.2-3.450.23691390.23752661X-RAY DIFFRACTION99.47
3.45-3.790.20071420.18612681X-RAY DIFFRACTION99.86
3.79-4.340.14681400.15022690X-RAY DIFFRACTION99.93
4.34-5.470.19391450.14872737X-RAY DIFFRACTION100
5.47-49.340.18131500.16882835X-RAY DIFFRACTION99.3
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)
12.7824196438-0.9050762745510.2540728789811.901590937340.07606034131783.939799574090.03882681704130.25580707449-0.113572853359-0.1618028105180.0142566003036-0.04707004205330.668800727220.2935449799672.30101018406E-50.818027571380.111631342964-0.01228060196740.69234591365-0.005303162445110.59007629458912.002752002157.69933576399.68043926302
21.8727128467-1.29705877405-0.1578303049041.440865514041.015086465521.49665074850.0446924626130.2131934325710.174474298417-0.1216320527360.00773635390020.250697785929-0.14748419353-0.6629681287470.0004154845255750.748758272660.113136977144-0.002203867895540.676204923490.02507374770390.621628501989-0.51028296137871.487161696718.7465615813
30.38758044941-0.382513337804-0.2217541813381.15408501302-0.4031464101320.6210090662690.273330167525-0.4068661406540.3143083369840.356948065881-0.2845446142040.467008456847-0.544870132808-0.9294933917260.0002968563466850.7658133324420.0689610953910.06001542946050.93005422556-0.05299319178070.684778136384-2.5680111938768.845068313634.041443865
41.80633775561-0.278227666968-0.1597692692281.851048116460.04084738111772.259811971620.119487465293-0.3879571248260.260138333763-0.0112479651993-0.0975918074424-0.218997700287-0.1205966103470.445220801242-0.000176842372870.8132276553670.0316001860665-0.01644542340330.649671962817-0.03101663760310.58342408494511.490625730571.606508061828.8904234903
52.04650555842-0.8545670539120.5280501669741.410854596741.183969510811.977786530880.0712168931693-0.290555652436-0.073581820131-0.05940509076470.0076421431807-0.1659262075870.5462513507440.6414546562580.0001675397033950.8963002542180.101391720465-0.04283267774140.847658762425-0.02381285826690.60165930018916.315618657260.440161135328.056070123
61.98296398428-0.3352340401180.0749216202080.0761408236043-0.03900374185430.587269590376-0.0680165225288-0.2730420406970.5758651915340.6697396033530.343528564117-0.72976368275-0.5022449439781.585632876610.0007760764880740.955986050325-0.0361694531855-0.06224290057521.34061896851-0.05370355377480.84950366188428.381647097668.160061534428.0439150318
70.0765183460203-0.137035054819-0.0541869510970.2416838861380.09726318352340.0364395311819-0.210222590216-0.388037438442-0.317476352123-0.3992886047330.461630466167-0.166455604202-0.957724661484-0.456198928177-0.0003690720376731.023456175080.3804863782170.02690570283121.253073522430.01799041254150.76559184992629.479169791942.935692108117.4723879672
80.535484721083-0.3565997621710.09595331925140.3402351404120.104664206960.2947933634760.166199402988-0.264252092055-0.2797062711830.336180815297-0.204975506522-0.463510110630.4703095818730.7954224698730.001278701290980.9429764854870.279278322608-0.05339902635450.8805893347950.06030738986350.71142079283721.808698432552.937130133224.7705000405
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 198 )78 - 1981 - 121
22chain 'A' and (resid 199 through 257 )199 - 257122 - 180
33chain 'A' and (resid 258 through 278 )258 - 278181 - 201
44chain 'A' and (resid 279 through 331 )279 - 331202 - 254
55chain 'A' and (resid 332 through 369 )332 - 369255 - 292
66chain 'A' and (resid 370 through 394 )370 - 394293 - 317
77chain 'A' and (resid 395 through 412 )395 - 412318 - 335
88chain 'A' and (resid 413 through 439 )413 - 439336 - 362

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