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- PDB-2y8v: Structure of chitinase, ChiC, from Aspergillus fumigatus. -

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Basic information

Entry
Database: PDB / ID: 2y8v
TitleStructure of chitinase, ChiC, from Aspergillus fumigatus.
ComponentsCLASS III CHITINASE, PUTATIVE
KeywordsHYDROLASE / AFCHIC
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsRush, C.L. / Schuettelkopf, A.W. / Gay, L.M. / van Aalten, D.M.F.
CitationJournal: To be Published
Title: Structure of Chitinase, Chic, from Aspergillus Fumigatus.
Authors: Rush, C.L. / Van Aalten, D.M.F.
History
DepositionFeb 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Atomic model
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLASS III CHITINASE, PUTATIVE
B: CLASS III CHITINASE, PUTATIVE
C: CLASS III CHITINASE, PUTATIVE
D: CLASS III CHITINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0355
Polymers130,0124
Non-polymers231
Water10,395577
1
A: CLASS III CHITINASE, PUTATIVE
B: CLASS III CHITINASE, PUTATIVE


Theoretical massNumber of molelcules
Total (without water)65,0062
Polymers65,0062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-34.3 kcal/mol
Surface area22880 Å2
MethodPISA
2
C: CLASS III CHITINASE, PUTATIVE
D: CLASS III CHITINASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0293
Polymers65,0062
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-44 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.137, 145.748, 82.899
Angle α, β, γ (deg.)90.00, 93.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A10 - 290
2115B10 - 290
3115C10 - 290
4115D10 - 290

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Components

#1: Protein
CLASS III CHITINASE, PUTATIVE / CHIC


Mass: 32502.998 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Strain: AF293 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4WEQ6, chitinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.12 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS PH 6.5, 28 % V/V PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.99→24.9 Å / Num. obs: 76641 / % possible obs: 89.5 % / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 63
Reflection shellResolution: 1.99→2.05 Å / Rmerge(I) obs: 0.17 / % possible all: 47.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.99→82.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.642 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21348 1507 2 %RANDOM
Rwork0.16871 ---
obs0.16959 75134 89.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20.01 Å2
2---0.94 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.99→82.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8817 0 1 577 9395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0229057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.95312323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3451114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19523.928443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.998151427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2271563
X-RAY DIFFRACTIONr_chiral_restr0.140.21289
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217113
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_it1.0661.55547
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83328898
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.18633510
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7354.53425
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1112medium positional0.230.5
2B1112medium positional0.240.5
3C1112medium positional0.260.5
4D1112medium positional0.270.5
1A1061loose positional0.635
2B1061loose positional0.545
3C1061loose positional0.565
4D1061loose positional0.595
1A1112medium thermal1.92
2B1112medium thermal1.182
3C1112medium thermal1.282
4D1112medium thermal1.752
1A1061loose thermal1.9710
2B1061loose thermal1.5810
3C1061loose thermal1.7510
4D1061loose thermal1.8910
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 46 -
Rwork0.174 3001 -
obs--47.89 %
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)
10.1301-0.16940.14550.5566-0.39830.48240.0045-0.01190.05050.02790.0241-0.056-0.0346-0.0594-0.02860.02660.01440.00320.04180.00440.055924.629157.531841.047
20.28310.1767-0.02290.4809-0.1170.45280.0306-0.0116-0.02950.0434-0.0141-0.0587-0.0034-0.0139-0.01650.006-0.0037-0.0030.03090.00780.023322.774823.262280.2856
30.2085-0.1996-0.20330.56650.46680.51430.0449-0.01020.0168-0.07180.0004-0.0356-0.03250.0053-0.04530.0228-0.00230.00420.0135-0.00910.012145.842361.372877.4072
40.24220.11780.07480.40390.1920.5698-0.01390.0162-0.0057-0.04150.0138-0.0026-0.00310.00770.00010.00550.0010.00050.0136-0.00080.000747.675219.409546.0269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 287
2X-RAY DIFFRACTION2B9 - 287
3X-RAY DIFFRACTION3C8 - 288
4X-RAY DIFFRACTION4D10 - 287

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