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- PDB-3w6d: Crystal structure of catalytic domain of chitinase from Ralstonia... -

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Basic information

Entry
Database: PDB / ID: 3w6d
TitleCrystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 (E141Q) in complex with tetrasaccharide
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 / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Chitin-binding domain type 3 / 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
triacetyl-beta-chitotriose / Lysozyme-like chitinolytic enzyme
Similarity search - Component
Biological speciesRalstonia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)84,4628
Polymers81,3424
Non-polymers3,1204
Water5,278293
1
A: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1662
Polymers20,3351
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1662
Polymers20,3351
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9632
Polymers20,3351
Non-polymers6281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1662
Polymers20,3351
Non-polymers8311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.369, 99.369, 242.795
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: 20335.465 Da / Num. of mol.: 4 / Fragment: catalytic domain, UNP residues 89-252 / Mutation: E141Q
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.13 Å3/Da / Density % sol: 42.17 % / Mosaicity: 0.258 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 11.1% (w/v) PEG 3350, 1.8% (v/v) isopropanol, 44.4mM CaCl2, 44.4mM HEPES (pH7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 21, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 39511 / Num. obs: 39480 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.3 % / Rmerge(I) obs: 0.078 / Χ2: 2.774 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.1918.80.35819212.0611100
2.19-2.2318.70.32719262.0851100
2.23-2.2718.40.29219262.1211100
2.27-2.3218.30.26819282.2081100
2.32-2.37180.24319512.2031100
2.37-2.4217.90.21819262.2851100
2.42-2.4817.60.19719422.2621100
2.48-2.5517.60.16119292.4071100
2.55-2.6217.20.14519442.51100
2.62-2.71170.12819472.611100
2.71-2.8116.80.11419472.731100
2.81-2.9216.60.09819712.828199.9
2.92-3.0516.50.0919543.0011100
3.05-3.2116.20.07919663.1321100
3.21-3.4116.20.0719833.3551100
3.41-3.6816.10.06119923.5199.9
3.68-4.0516.20.05419953.693199.9
4.05-4.6316.70.05120293.689199.9
4.63-5.8317.80.05120723.608199.9
5.83-5017.20.04622313.391199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W6B

3w6b


Resolution: 2.15→42.34 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2195 / WRfactor Rwork: 0.1791 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8733 / SU B: 9.767 / SU ML: 0.122 / SU R Cruickshank DPI: 0.2287 / SU Rfree: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1974 5 %RANDOM
Rwork0.1821 ---
obs0.184 39246 99.58 %-
all-39511 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.94 Å2 / Biso mean: 31.6592 Å2 / Biso min: 12.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4783 0 214 293 5290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215140
X-RAY DIFFRACTIONr_angle_refined_deg0.981.9876959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7445608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38823.559236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20815732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5561524
X-RAY DIFFRACTIONr_chiral_restr0.0670.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213975
X-RAY DIFFRACTIONr_mcbond_it0.3161.53011
X-RAY DIFFRACTIONr_mcangle_it0.62224774
X-RAY DIFFRACTIONr_scbond_it1.10832129
X-RAY DIFFRACTIONr_scangle_it1.6354.52185
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 136 -
Rwork0.21 2705 -
all-2841 -
obs--99.34 %
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)
11.25810.79620.43951.38360.80412.40760.0220.0436-0.0869-0.29970.13470.0027-0.25360.2796-0.15680.39920.0258-0.0590.0745-0.07290.1399-11.003-8.991-12.044
21.6254-0.4144-0.71761.48071.37953.10230.0991-0.0086-0.1055-0.1652-0.17580.0243-0.4702-0.38250.07670.2030.07810.06420.077-0.02420.104710.86-29.1960.534
32.5902-0.02030.63032.6473-0.00250.70970.1054-0.21770.06260.0331-0.0084-0.00460.0801-0.1088-0.0970.16020.017-0.07970.0305-0.00950.1228-34.007-24.9650.43
41.7198-0.3799-0.48531.06660.16982.40450.04320.0171-0.04670.0462-0.01470.0657-0.23110.0688-0.02850.0918-0.02820.04020.0570.00210.101927.652-37.61-23.248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A102 - 254
2X-RAY DIFFRACTION2B102 - 254
3X-RAY DIFFRACTION3C102 - 254
4X-RAY DIFFRACTION4D102 - 254

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