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- PDB-3vvg: The Crystal Structure of Cellulase-Inhibitor Complex. -

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Basic information

Entry
Database: PDB / ID: 3vvg
TitleThe Crystal Structure of Cellulase-Inhibitor Complex.
Components458aa long hypothetical endo-1,4-beta-glucanase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Cellulase Inhibition / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
CGP-CTERM domain / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 3-(4-methoxy-3-methylphenyl)propanoic acid / 458aa long hypothetical endo-1,4-beta-glucanase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIshikawa, K. / Maeno, Y. / Kataoka, M.
CitationJournal: TO BE PUBLISHED
Title: The Crystal Structure of Cellulase-Inhibitor Complex.
Authors: Ishikawa, K. / Maeno, Y. / Kataoka, M.
History
DepositionJul 24, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 458aa long hypothetical endo-1,4-beta-glucanase
B: 458aa long hypothetical endo-1,4-beta-glucanase
C: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,83410
Polymers129,8723
Non-polymers9637
Water12,250680
1
A: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7744
Polymers43,2911
Non-polymers4833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5764
Polymers43,2911
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 458aa long hypothetical endo-1,4-beta-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4852
Polymers43,2911
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.566, 58.433, 138.008
Angle α, β, γ (deg.)90.00, 109.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 458aa long hypothetical endo-1,4-beta-glucanase


Mass: 43290.621 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 34-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT-3 / Gene: PH1171 / Production host: Escherichia coli (E. coli) / References: UniProt: O58925
#2: Chemical ChemComp-ZGB / 3-(4-methoxy-3-methylphenyl)propanoic acid


Mass: 194.227 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H14O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M zinc acetate, 0.1M MES buffer pH6.0, 15%(v/v) ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→130.19 Å / Num. all: 208594 / Num. obs: 95782 / % possible obs: 98.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 17

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0066refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.885 / SU B: 4.317 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28559 4855 5 %RANDOM
Rwork0.21951 ---
obs0.22278 91820 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.722 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20.83 Å2
2--0.17 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9207 0 56 680 9943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0229585
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.92813083
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14351126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80824.418464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.938151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9711526
X-RAY DIFFRACTIONr_chiral_restr0.1490.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217539
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2071.55607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92629071
X-RAY DIFFRACTIONr_scbond_it2.94333978
X-RAY DIFFRACTIONr_scangle_it4.034.54012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 342 -
Rwork0.264 6346 -
obs--93.56 %

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