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- PDB-1wzx: Crystal Structure of Family 30 Carbohydrate Binding Module. -

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Basic information

Entry
Database: PDB / ID: 1wzx
TitleCrystal Structure of Family 30 Carbohydrate Binding Module.
ComponentsCOG3291: FOG: PKD repeat
KeywordsSUGAR BINDING PROTEIN / CBM30 / Carbohydrate Binding Module Family30 / CelJ
Function / homology
Function and homology information


cellulase activity / cellulose catabolic process / metal ion binding
Similarity search - Function
: / Carbohydrate binding domain 30 / Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Galactose-binding lectin / PKD domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 ...: / Carbohydrate binding domain 30 / Glycoside hydrolase, family 44 / Glycoside hydrolase family 44 / Cellulase N-terminal ig-like domain / Cellulase, Ig-like domain / Galactose-binding lectin / PKD domain / Glycoside hydrolase family 9 / Glycosyl hydrolase family 9 / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Immunoglobulin E-set / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Glycoside hydrolase family 9
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsHoriguchi, Y. / Kono, M. / Suzuki, A. / Yamane, T. / Arai, M. / Sakka, K. / Omiya, K.
CitationJournal: To be Published
Title: Crystal Structure of Family 30 Carbohydrate Binding Module
Authors: Horiguchi, Y. / Kono, M. / Suzuki, A. / Yamane, T. / Arai, M. / Sakka, K. / Omiya, K.
History
DepositionMar 10, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COG3291: FOG: PKD repeat
B: COG3291: FOG: PKD repeat
C: COG3291: FOG: PKD repeat
D: COG3291: FOG: PKD repeat


Theoretical massNumber of molelcules
Total (without water)92,5364
Polymers92,5364
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.106, 121.106, 122.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 8 - 180 / Label seq-ID: 8 - 180

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
COG3291: FOG: PKD repeat / family 30 carbohydrate binding module


Mass: 23134.041 Da / Num. of mol.: 4 / Fragment: residues 1-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Plasmid: pCBM / Production host: Escherichia coli (E. coli) / References: GenBank: 48859367, UniProt: A3DD30*PLUS

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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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.79
Details: 0.1M MES, 1.2M Ammonium Sulfate, 10% Dioxane, pH 5.79, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→104.83 Å / Num. obs: 14792 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.147
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 13 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WMX

1wmx


Resolution: 3.52→20.83 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.797 / SU B: 39.606 / SU ML: 0.609 / Cross valid method: THROUGHOUT / ESU R Free: 0.726 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29436 623 4.9 %RANDOM
Rwork0.20599 ---
all0.21043 ---
obs0.21043 12026 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.654 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0.32 Å20 Å2
2---0.64 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 3.52→20.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5564 0 0 0 5564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0225700
X-RAY DIFFRACTIONr_angle_refined_deg3.1151.9427776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.7255691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52824.496258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.38715936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4031525
X-RAY DIFFRACTIONr_chiral_restr0.2060.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024285
X-RAY DIFFRACTIONr_nbd_refined0.3520.23394
X-RAY DIFFRACTIONr_nbtor_refined0.3720.23955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2830.2284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.22
X-RAY DIFFRACTIONr_mcbond_it1.0921.53540
X-RAY DIFFRACTIONr_mcangle_it1.95125628
X-RAY DIFFRACTIONr_scbond_it2.00232598
X-RAY DIFFRACTIONr_scangle_it3.1044.52148
Refine LS restraints NCS

Ens-ID: 1 / Number: 692 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.150.05
2Btight positional0.130.05
3Ctight positional0.130.05
4Dtight positional0.130.05
1Amedium positional0.890.5
2Bmedium positional0.720.5
3Cmedium positional0.880.5
4Dmedium positional0.80.5
1Atight thermal0.190.5
2Btight thermal0.170.5
3Ctight thermal0.180.5
4Dtight thermal0.20.5
1Amedium thermal1.212
2Bmedium thermal1.092
3Cmedium thermal1.212
4Dmedium thermal1.362
LS refinement shellResolution: 3.522→3.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 52 -
Rwork0.3 700 -
obs--80.77 %

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