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- PDB-9r4p: Crystal structure of inactive (D164N) variant CtGH76 from Chaetom... -

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Basic information

Entry
Database: PDB / ID: 9r4p
TitleCrystal structure of inactive (D164N) variant CtGH76 from Chaetomium thermophilum in complex with alpha-1,6-mannobiose
ComponentsCtGH76
KeywordsHYDROLASE / Glycoside Hydrolases / carbohydrate-binding protein
Function / homology: / Glycoside hydrolase, family 76 / Glycosyl hydrolase family 76 / Six-hairpin glycosidase superfamily / carbohydrate metabolic process / 6alpha-alpha-mannobiose / alpha-D-mannopyranose / Uncharacterized protein
Function and homology information
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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: CtGH76
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7914
Polymers48,0881
Non-polymers7033
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.090, 107.090, 127.267
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 CtGH76


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, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6alpha-alpha-mannobiose
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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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 / Density % sol: 71.92 %
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: 2.46→49.35 Å / Num. obs: 30958 / % possible obs: 99.31 % / Redundancy: 20 % / Biso Wilson estimate: 59.15 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 12.82
Reflection shellResolution: 2.46→2.548 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 3035 / CC1/2: 0.593

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→49.35 Å / SU ML: 0.3356 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 1546 5 %
Rwork0.2013 29403 -
obs0.2022 30949 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.13 Å2
Refinement stepCycle: LAST / Resolution: 2.46→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 47 36 2895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582921
X-RAY DIFFRACTIONf_angle_d0.70723986
X-RAY DIFFRACTIONf_chiral_restr0.0432445
X-RAY DIFFRACTIONf_plane_restr0.0054514
X-RAY DIFFRACTIONf_dihedral_angle_d12.0979439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.540.43411370.41212581X-RAY DIFFRACTION97.04
2.54-2.630.3731390.36042651X-RAY DIFFRACTION99.64
2.63-2.730.34931390.33122639X-RAY DIFFRACTION99.25
2.73-2.860.3141390.28422646X-RAY DIFFRACTION99.61
2.86-3.010.2991370.24782636X-RAY DIFFRACTION99.04
3.01-3.20.29741400.25052653X-RAY DIFFRACTION99.22
3.2-3.450.25171390.23862688X-RAY DIFFRACTION99.75
3.45-3.790.17711410.18112659X-RAY DIFFRACTION99.4
3.79-4.340.15281410.15122670X-RAY DIFFRACTION99.22
4.34-5.470.19011450.15112745X-RAY DIFFRACTION100
5.47-49.350.19191490.17482835X-RAY DIFFRACTION99.33
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)
12.91395835629-0.8099071843650.3675759418412.111658136160.5073191769764.06494263030.009910335788580.518850467384-0.233412406262-0.1971952390260.0588255516928-0.02139377006040.8769322912990.5973792893859.68509545038E-51.015615752610.124926669222-0.001712715361050.851801690987-0.01999736626790.72846877227514.552443069554.366034248710.3498154326
20.925194385915-0.1974038735030.3684123340711.385336786170.8011309973521.025010955610.151154679390.25141462274-0.0254084956536-0.225982739252-0.0730352708148-0.0746802465923-0.2350499161440.02300803302420.0006470394758130.8219638724260.06864388928680.009759284571280.8393821159560.01894778721270.7250902644056.2376949182665.29694102388.36860371778
32.07346387273-1.45949861420.1863090694882.304873437441.334096206492.456399001460.08428502723310.131892685940.0462029502902-0.102092012498-0.07322087093660.263554720518-0.403186385893-0.4809912560320.0009147030887390.8389981344320.0558215177567-0.003136891105910.706429374822-0.007070879847780.678338093964-0.60776992319771.561218164218.6167718444
42.068352802030.337951456031-0.2213004398922.645655637670.04444102555494.179648326670.12617322459-0.4429169695790.170048716320.123969277457-0.182109747334-0.0498573427794-0.3386298436570.3409091762347.04508566213E-50.9267062392230.000660314666574-0.008580981317540.733120414582-0.03997522084360.6811927369417.5420958722971.022155064630.1864930774
51.84675920028-0.4916371858450.3502063412041.530059194021.686853947742.214601425450.275968954411-0.6105234354730.1008114940880.230954963606-0.3373457642360.0411704582480.4234393124640.957123192826-0.001738974616821.013606479030.0486213233598-0.01994033983161.03530774135-0.01768799646940.77187017779716.203249214260.616291283628.0851767294
61.69056341993-0.07741037703320.2510971952370.006347995640560.01112818629230.643662718326-0.101055835667-0.2037772655190.7431815934140.1404238083020.344821230991-0.833555592374-0.3256023355591.17872732929-0.0003302750871660.988860994346-0.114298886699-0.0461192809291.54923268541-0.01350564016471.0240025238828.185471726868.333110865728.0409371695
70.2305123463030.000276692485709-0.1407016304490.01090942079020.01348057507150.0692038500629-0.432500166519-0.233695292875-0.208587646394-0.8560023466250.7344711023580.141069028594-1.401976224740.107762735945-0.0001210026144891.073253789130.326276364186-0.0326161630311.42103351676-0.03894589647630.79158443155529.314710119543.074917856617.6274961111
81.07155184419-0.472798132960.08256743322920.4291562756250.2745614436230.7465886515340.102798959076-0.0896667798794-0.3622533372130.2389065724120.0198451189291-0.3660250362160.429194295720.7963288892480.0002173100780771.068651732940.212139717376-0.05829027075171.078200409910.000272243518620.8515207680621.956163359453.106192021724.8507815657
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 198 )162 - 19885 - 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 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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