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- PDB-3w6b: Crystal structure of catalytic domain of chitinase from Ralstonia... -

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Basic information

Entry
Database: PDB / ID: 3w6b
TitleCrystal structure of catalytic domain of chitinase from Ralstonia sp. A-471
ComponentsLysozyme-like chitinolytic enzyme
KeywordsHYDROLASE / GH family 23 / enzyme / Glycoside hydrolase / chitinase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Lysozyme-like chitinolytic enzyme
Similarity search - Component
Biological speciesRalstonia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsArimori, T. / Kawamoto, N. / Okazaki, N. / Nakazawa, M. / Miyatake, K. / Fukamizo, T. / Ueda, M. / Tamada, T.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structures of the Catalytic Domain of a Novel Glycohydrolase Family 23 Chitinase from Ralstonia sp. A-471 Reveals a Unique Arrangement of the Catalytic Residues for Inverting Chitin Hydrolysis
Authors: Arimori, T. / Kawamoto, N. / Shinya, S. / Okazaki, N. / Nakazawa, M. / Miyatake, K. / Fukamizo, T. / Ueda, M. / Tamada, T.
History
DepositionFeb 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Lysozyme-like chitinolytic enzyme
B: Lysozyme-like chitinolytic enzyme
C: Lysozyme-like chitinolytic enzyme
D: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7148
Polymers81,3464
Non-polymers3684
Water4,252236
1
A: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4292
Polymers20,3361
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme-like chitinolytic enzyme


Theoretical massNumber of molelcules
Total (without water)20,3361
Polymers20,3361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4292
Polymers20,3361
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5213
Polymers20,3361
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.660, 99.660, 242.464
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Lysozyme-like chitinolytic enzyme


Mass: 20336.449 Da / Num. of mol.: 4 / Fragment: catalytic domain, UNP residues 89-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia (bacteria) / Strain: A-471 / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: B7XCV4, chitinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.43 % / Mosaicity: 0.374 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5% (w/v) PEG 8000, 167mM (NH4)3-citrate/ammonium hydroxide (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL38B120.9950, 0.9789, 0.9730, 0.9641
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDMar 5, 2009
ADSC QUANTUM 2102CCDDec 3, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9951
30.97891
40.9731
50.96411
ReflectionResolution: 1.9→100 Å / Num. all: 57014 / Num. obs: 55600 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Rmerge(I) obs: 0.076 / Χ2: 1.338 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.978.30.39853290.688195.5
1.97-2.0511.40.36753770.759196.5
2.05-2.1413.10.31554220.835196.9
2.14-2.2514.50.2654680.942197.3
2.25-2.3915.50.20854821.008197.5
2.39-2.5816.60.16255181.114197.8
2.58-2.8417.90.11655741.264198.2
2.84-3.2519.20.08556301.562198.5
3.25-4.0920.40.0657422.011198.8
4.09-10019.70.04660581.996198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→32.62 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.103 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 2825 5.1 %RANDOM
Rwork0.1853 ---
obs0.1875 55598 97.69 %-
all-57014 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 77.24 Å2 / Biso mean: 32.2639 Å2 / Biso min: 15.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4834 0 24 236 5094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224990
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.9496766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70323.586237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57815735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0711524
X-RAY DIFFRACTIONr_chiral_restr0.1250.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213948
X-RAY DIFFRACTIONr_mcbond_it1.0791.53051
X-RAY DIFFRACTIONr_mcangle_it1.82724845
X-RAY DIFFRACTIONr_scbond_it3.02331939
X-RAY DIFFRACTIONr_scangle_it4.3694.51921
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 170 -
Rwork0.282 3734 -
all-3904 -
obs--94.73 %
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)
10.64310.3044-0.27210.23770.04250.5559-0.0287-0.04010.07260.04020.0810.05860.04960.1294-0.05230.0740.08540.05980.14440.02160.113986.3115-4.260551.9749
20.65410.0329-0.69950.51660.31320.9962-0.14140.0003-0.051-0.02040.0340.0570.16550.0250.10730.08060.0322-0.00350.066-0.06730.107279.817224.178439.9221
30.6987-0.38240.25831.3167-0.42170.1785-0.0322-0.094-0.0646-0.12740.06220.04970.0344-0.0183-0.030.0680.05570.0450.08840.06530.087161.0364-17.495139.8314
40.31760.0746-0.16850.84450.2260.89530.0623-0.0055-0.05160.0398-0.01950.0471-0.05450.097-0.04270.0478-0.0155-0.02260.0694-0.03310.066480.965242.881263.5731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A95 - 254
2X-RAY DIFFRACTION2B102 - 254
3X-RAY DIFFRACTION3C102 - 254
4X-RAY DIFFRACTION4D102 - 254

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