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- PDB-9r4n: Crystal structure of CtGH76 from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 9r4n
TitleCrystal structure of CtGH76 from Chaetomium thermophilum
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 / FORMIC ACID / alpha-D-mannopyranose / Uncharacterized protein
Function and homology information
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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)48,7505
Polymers48,0891
Non-polymers6614
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint8 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.531, 107.531, 127.193
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 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+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

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Non-polymers , 3 types, 33 molecules

#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: 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.: 31 / 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: 4.41 Å3/Da / Density % sol: 72.14 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 21, 2020
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.55→49.52 Å / Num. obs: 28133 / % possible obs: 99.64 % / Redundancy: 2 % / Biso Wilson estimate: 56.45 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.03665 / Rrim(I) all: 0.05183 / Net I/σ(I): 7.01
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 2 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 2783 / CC1/2: 0.955 / CC star: 0.988 / Rrim(I) all: 0.2573 / % possible all: 99.68

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→49.52 Å / SU ML: 0.3002 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 1386 4.93 %
Rwork0.2052 26739 -
obs0.2067 28125 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.52 Å2
Refinement stepCycle: LAST / Resolution: 2.55→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 44 31 2887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242927
X-RAY DIFFRACTIONf_angle_d0.48693993
X-RAY DIFFRACTIONf_chiral_restr0.0373441
X-RAY DIFFRACTIONf_plane_restr0.0043517
X-RAY DIFFRACTIONf_dihedral_angle_d7.7175411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.640.3151340.30682647X-RAY DIFFRACTION99.64
2.64-2.750.33421380.26542615X-RAY DIFFRACTION99.78
2.75-2.870.27011350.25572671X-RAY DIFFRACTION99.57
2.87-3.020.33271030.23622654X-RAY DIFFRACTION99.71
3.02-3.210.25851610.25742619X-RAY DIFFRACTION99.18
3.21-3.460.2851110.23982675X-RAY DIFFRACTION99.36
3.46-3.810.23141440.20092654X-RAY DIFFRACTION99.82
3.81-4.360.2241500.16452672X-RAY DIFFRACTION99.79
4.36-5.490.22521390.17292723X-RAY DIFFRACTION99.65
5.49-49.520.19271710.19672809X-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)
12.39915888256-0.0318598616138-0.1911275450852.111257139220.3621695574654.38138969464-0.07312509407280.0944988781741-0.333910688843-0.281360675630.121699063772-0.02738303651750.7442659582330.599536499434-6.50201683136E-50.7702764315310.1527616191430.01930278176680.683596179057-0.01360922567210.65305827482314.723110760454.566419054510.2593702731
20.944598551791-0.439312006090.4835529139141.818663384330.4347960447091.85803028168-0.06413194373870.1117698637970.01401071697710.002653274471850.01541982042110.1365682153090.0341072712889-0.219488043645-3.47458387929E-50.6229016938380.052893023648-0.03919724065950.6473060616570.02088269105550.6530374975081.4338357800565.677971073913.1160195688
30.792515947877-0.186358251293-0.271758201580.6290789730820.7488479492010.8838657495690.3234258365710.3881806137220.343699630701-0.12844056207-0.2295476906890.106479044892-0.945301902406-0.1549128316786.0856306037E-50.8634207375420.1060788130330.05012223774340.533071578224-0.0006823464532710.6674277754143.6711806133575.344988149616.3238727278
41.64895349553-0.642469804274-0.06094723037952.66909570638-0.605952775044.855836034450.108583870444-0.5157938608540.2114760836140.165037293797-0.142413624843-0.151348832526-0.5016752467530.4022190305297.34326611741E-50.692018789834-0.0325977949936-0.001432335893360.588264850396-0.05830360038230.6033982111437.4990192566271.31044838330.2253907649
52.48612034542-0.9232284660170.4375380351491.361351798271.248832327932.010861777860.305233639911-0.6021292443920.01430307927020.0304512828786-0.295677919690.1382157029130.3857952981241.00118225067-0.000281983535350.8132434112690.0613858690678-0.02546469506030.889385205059-0.02796283428830.62819549439316.161619513760.826199305328.080640457
61.792195973980.02691252430590.3658432975920.02748714945530.1913301455241.296346271040.294129658046-0.3796215753150.492285364191-0.667318436918-0.0868926692131-0.703606842436-0.3443096963721.6553968942-0.002559435953740.805627827734-0.04112079352070.01057286368671.558735006150.01844831429170.91209210667328.442438875165.388436514427.6457643481
71.54102050857-0.623281112226-0.8226199691630.8268469358880.7279553012940.675793742329-0.167618548989-0.18042014294-0.1965842463360.3547228606420.200139230162-0.06202744893610.2940941311920.571532447015-8.26922482209E-50.8235613424380.251605301131-0.002793975724361.042179873610.06957388683520.71006904307324.405255321749.230819875621.5711655363
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 219 )162 - 21985 - 142
33chain 'A' and (resid 220 through 256 )220 - 256143 - 179
44chain 'A' and (resid 257 through 331 )257 - 331180 - 254
55chain 'A' and (resid 332 through 369 )332 - 369255 - 292
66chain 'A' and (resid 370 through 398 )370 - 398293 - 321
77chain 'A' and (resid 399 through 439 )399 - 439322 - 362

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