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- PDB-3w6f: Crystal structure of catalytic domain of chitinase from Ralstonia... -

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Basic information

Entry
Database: PDB / ID: 3w6f
TitleCrystal structure of catalytic domain of chitinase from Ralstonia sp. A-471 (E162Q) in complex with disaccharide
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
Lysozyme-like chitinolytic enzyme
Similarity search - Component
Biological speciesRalstonia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / 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_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.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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)84,31311
Polymers81,3424
Non-polymers2,9717
Water3,657203
1
A: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1843
Polymers20,3351
Non-polymers8492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1843
Polymers20,3351
Non-polymers8492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7602
Polymers20,3351
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lysozyme-like chitinolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1843
Polymers20,3351
Non-polymers8492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.304, 99.304, 242.406
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: E162Q
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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.12 Å3/Da / Density % sol: 42 % / Mosaicity: 0.311 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8.9% (w/v) PEG 8000, 8.9% (v/v) PEG400, 44.4mM MgCl2, 44.4mM Tris-Cl (pH8.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 42173 / Num. obs: 42007 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.103 / Χ2: 2.096 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.146.20.37720360.848199.7
2.14-2.186.40.35120550.911199.3
2.18-2.226.50.33120450.944199.5
2.22-2.266.80.3220761.028199.6
2.26-2.3170.29320401.099199.5
2.31-2.377.10.27520611.096199.8
2.37-2.427.20.2620561.179199.8
2.42-2.497.50.24120701.28199.7
2.49-2.567.80.21120571.441199.6
2.56-2.657.90.18620801.565199.9
2.65-2.748.10.16820681.686199.6
2.74-2.858.40.15620861.842199.7
2.85-2.988.60.13721042.064199.9
2.98-3.148.80.12420912.291199.8
3.14-3.3390.10821092.647199.8
3.33-3.599.10.09421193.025199.7
3.59-3.9590.08121273.423199.8
3.95-4.5290.07321813.687199.7
4.52-5.790.0721813.485199.7
5.7-508.20.06223653.491198.8

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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: 2.1→49.65 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.1832 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8544 / SU B: 11.743 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2205 / SU Rfree: 0.1869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 2112 5.1 %RANDOM
Rwork0.1981 ---
obs0.2003 41777 99.29 %-
all-42173 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.7 Å2 / Biso mean: 36.5174 Å2 / Biso min: 14.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4740 0 203 203 5146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215082
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.9866888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.835603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62223.675234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16815723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1121522
X-RAY DIFFRACTIONr_chiral_restr0.0670.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213936
X-RAY DIFFRACTIONr_mcbond_it0.3961.52985
X-RAY DIFFRACTIONr_mcangle_it0.76324730
X-RAY DIFFRACTIONr_scbond_it1.16332097
X-RAY DIFFRACTIONr_scangle_it1.7444.52158
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 144 -
Rwork0.282 2877 -
all-3021 -
obs--99.08 %
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)
10.14220.3062-0.03180.98391.34361.94170.0512-0.1281-0.1359-0.23740.09310.1338-0.28980.2958-0.14430.37320.0434-0.08150.0038-0.14290.2347-11.26-8.977-11.861
20.5275-0.2738-0.24040.66211.48792.32490.1184-0.0893-0.1818-0.1124-0.1924-0.0437-0.3542-0.35990.0740.24360.08310.09080.1271-0.02670.216510.861-29.2780.658
31.4866-0.34490.37111.508-0.76160.3131-0.1375-0.29670.0054-0.23140.14730.1083-0.0356-0.0835-0.00980.23130.0747-0.13150.0561-0.02160.2579-34.043-24.5950.676
40.9359-0.4202-0.34960.50330.17221.8070.0070.061-0.06210.038-0.00230.0656-0.10440.0811-0.00470.1174-0.0170.03720.0988-0.00480.282627.66-37.564-23.11
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A103 - 252
2X-RAY DIFFRACTION2B102 - 254
3X-RAY DIFFRACTION3C103 - 253
4X-RAY DIFFRACTION4D102 - 254

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