[English] 日本語
Yorodumi
- PDB-9r4r: Crystal structure of CtGH76 from Chaetomium thermophilum in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r4r
TitleCrystal structure of CtGH76 from Chaetomium thermophilum in complex with glucosamine
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 / 2-amino-2-deoxy-alpha-D-glucopyranose / Uncharacterized protein
Function and homology information
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chains: A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7758
Polymers48,0891
Non-polymers6867
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint2 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.128, 108.128, 128.633
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

-
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: Sugar ChemComp-PA1 / 2-amino-2-deoxy-alpha-D-glucopyranose / alpah-D-glucosamine / 2-amino-2-deoxy-alpha-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose


Type: D-saccharide, alpha linking / Mass: 179.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.51 Å3/Da / Density % sol: 72.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.6 M sodium formate 10% (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 21, 2024
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.35→46.82 Å / Num. obs: 36013 / % possible obs: 97.86 % / Redundancy: 10.2 % / Biso Wilson estimate: 60.97 Å2 / CC1/2: 0.997 / Net I/σ(I): 8.73
Reflection shellResolution: 2.35→2.434 Å / Mean I/σ(I) obs: 0.36 / Num. unique obs: 2969 / CC1/2: 0.585

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.82 Å / SU ML: 0.4065 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.6839
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 1781 4.95 %
Rwork0.2014 34232 -
obs0.2025 36013 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.01 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 45 101 2958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022932
X-RAY DIFFRACTIONf_angle_d0.46973992
X-RAY DIFFRACTIONf_chiral_restr0.0365432
X-RAY DIFFRACTIONf_plane_restr0.0046520
X-RAY DIFFRACTIONf_dihedral_angle_d6.4799410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.4906860.47892155X-RAY DIFFRACTION80.04
2.41-2.480.4261170.41562555X-RAY DIFFRACTION96.46
2.48-2.560.36481640.36242624X-RAY DIFFRACTION99.71
2.56-2.660.36511250.35642653X-RAY DIFFRACTION99.82
2.66-2.760.36831350.34022670X-RAY DIFFRACTION99.89
2.76-2.890.27871430.27122645X-RAY DIFFRACTION99.82
2.89-3.040.30731370.24952623X-RAY DIFFRACTION98.75
3.04-3.230.2351330.22232688X-RAY DIFFRACTION99.89
3.23-3.480.28471330.20842690X-RAY DIFFRACTION100
3.48-3.830.20661720.17062647X-RAY DIFFRACTION99.96
3.83-4.380.16041320.13662701X-RAY DIFFRACTION100
4.39-5.520.1411580.14832728X-RAY DIFFRACTION100
5.52-46.820.21261460.17492853X-RAY DIFFRACTION99.87
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)
11.74359353903-0.854827771149-0.6679130882541.95238992272-0.4501654309634.100035971050.0153166097577-0.0208363244593-0.111747521333-0.216141770621-0.101237872206-0.120028244860.7800609141560.9809786057130.0001555887163560.724898626560.2641717175510.03803775885280.673391343145-0.003083095486080.58619610203719.220157307454.103923217713.7716632122
21.83199898789-0.277863827564-0.6010592793121.78067552018-0.09980764020754.20802306976-0.1037534773080.288980320811.07121041788E-5-0.2757640527660.07736108702620.09692697432750.3874507633150.04196981602089.44109090426E-60.5741839265630.0739020847809-0.02836401351140.515235796219-0.04051410932080.5521175167397.3315213481361.38522211076.93215149031
32.11717654698-0.5964751843640.1525337090151.661053672921.328809463423.357888321660.1297747058020.1390887703830.149358473402-0.130922858112-0.02125925812440.314502893955-0.412837351091-0.397928516213-9.84083948364E-50.5685136926750.098158883648-0.01079382893280.430016261766-0.006786269757410.601600781112-0.7707669144172.51525381818.5912220363
41.89558993739-0.444572897359-0.5021839203551.715759034720.2573578021385.31589613930.200624726852-0.3968909335570.06599087181470.230346072067-0.1189954588940.0546579631794-0.4766162990780.391846675525.39586966028E-50.577138978082-0.03577797772530.008161658066060.482219058039-0.04783006697230.5580746662347.4279220755471.702552735730.4185583534
51.66835930609-1.183884062060.1329969574931.568495701431.438709175224.769254791170.141664872425-0.4903229661040.134430242817-0.0603496873533-0.229237359149-0.2050406268240.1776190466311.436090657810.0005982420778340.5683501434570.0535367110534-0.04493382753051.012341235460.004932022224750.61648583165721.245661501764.403152675928.3175415929
60.5045557034230.8165446331610.1812014900792.631977073511.213778374650.710051257021-0.320113058417-0.259439803979-0.630739529611-0.5472913662490.7436394912050.148256485788-1.07021558403-0.615486500290.0687938650750.917935358280.357074843546-0.01096189170931.194355773960.07978796414220.75935461568929.581615625743.505935615517.7678528121
70.603557784531-0.0506538114104-0.3185602350520.375537981944-0.3885634245220.8944018937890.188612297324-0.233073920486-0.1662713192770.350680935426-0.257513832325-0.1737096990650.6845135817471.42264587576-0.007969390861530.8191889925670.362772626581-0.03549424397570.8977100561420.02704730161230.6586138447721.732294050153.598613889225.0676499735
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more