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- PDB-4txg: Crystal Structure of a Family GH18 Chitinase from Chromobacterium... -

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Basic information

Entry
Database: PDB / ID: 4txg
TitleCrystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum
ComponentsChitinase
KeywordsHYDROLASE / Chitinase Family GH18 Chitinase
Function / homology
Function and homology information


chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region
Similarity search - Function
Chitinase, C-terminal / Chitinase C / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II ...Chitinase, C-terminal / Chitinase C / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Probable chitinase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.75 Å
AuthorsPereira, H.M. / Teixeira, C.S. / Grangeiro, T.B.
CitationJournal: To Be Published
Title: Crystal Structure of a Family GH18 Chitinase from Chromobacterium violaceum
Authors: Pereira, H.M. / Teixeira, C.S. / Grangeiro, T.B.
History
DepositionJul 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,66815
Polymers84,8071
Non-polymers1,86114
Water18,1231006
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-436 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.866, 126.866, 93.815
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Chitinase


Mass: 84807.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria)
Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757
Gene: CV_3316 / Plasmid: pPICZalphaA / Production host: Komagataella pastoris GS115 (fungus) / Strain (production host): GS115 / References: UniProt: Q7NSV3
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cs
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200mM Litium Sulphate, 100mM Hepes pH 7.5, 25% Peg 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2011
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 169502 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge F obs: 0.103 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.084 / Χ2: 1.19 / Net I/σ(I): 16.48 / Num. measured all: 1085043
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.75-1.792.50.6610.4252.373023312686116670.52992
1.79-1.840.5080.3893.274284312291121220.45998.6
1.84-1.90.3280.3344.876085812013119760.37399.7
1.9-1.950.2240.2676.717072311698116460.29299.6
1.95-2.020.180.2258.047017811235112160.24599.8
2.02-2.090.1460.18310.017045210905108780.19999.8
2.09-2.170.1210.15811.657074610499104920.17199.9
2.17-2.260.1030.14113.477077310143101340.15299.9
2.26-2.360.0890.12715.1371405977097670.137100
2.36-2.470.0770.11317.0369837924792460.121100
2.47-2.610.0660.119.0167315883588340.107100
2.61-2.760.0560.08621.7263769835583540.092100
2.76-2.960.0490.07524.3559649782578240.081100
2.96-3.190.0390.06228.6555376730172990.067100
3.19-3.50.0310.05332.7950577673867380.057100
3.5-3.910.0260.04536.945391607360730.048100
3.91-4.510.0210.0440.640255536253600.043100
4.51-5.530.020.03841.3134000450644990.04199.8
5.53-7.820.0190.0440.9426543349234900.04399.9
7.820.0160.03645.5114120191418870.03998.6

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXDEphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
GDAdata collection
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→37.973 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 16.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1758 8483 5 %Random selection
Rwork0.1572 161016 --
obs0.1581 169499 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 334.47 Å2 / Biso mean: 17.8856 Å2 / Biso min: 5.13 Å2
Refinement stepCycle: final / Resolution: 1.75→37.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5181 0 14 1006 6201
Biso mean--121.06 31.18 -
Num. residues----679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065330
X-RAY DIFFRACTIONf_angle_d1.0347267
X-RAY DIFFRACTIONf_chiral_restr0.044756
X-RAY DIFFRACTIONf_plane_restr0.005957
X-RAY DIFFRACTIONf_dihedral_angle_d11.8821864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76780.25242390.22654600X-RAY DIFFRACTION84
1.7678-1.78860.222760.21155253X-RAY DIFFRACTION97
1.7886-1.81050.23422770.20275299X-RAY DIFFRACTION98
1.8105-1.83340.20522810.19565362X-RAY DIFFRACTION99
1.8334-1.85750.19962840.18565410X-RAY DIFFRACTION100
1.8575-1.88290.19022820.17345344X-RAY DIFFRACTION99
1.8829-1.90980.1892830.17165356X-RAY DIFFRACTION100
1.9098-1.93830.18742850.16075415X-RAY DIFFRACTION100
1.9383-1.96860.18712860.15595421X-RAY DIFFRACTION100
1.9686-2.00090.19652820.16275392X-RAY DIFFRACTION100
2.0009-2.03540.18312860.15365409X-RAY DIFFRACTION100
2.0354-2.07240.17412860.14815410X-RAY DIFFRACTION100
2.0724-2.11230.16872840.1515419X-RAY DIFFRACTION100
2.1123-2.15540.19852820.14965394X-RAY DIFFRACTION100
2.1554-2.20220.20062810.15395354X-RAY DIFFRACTION100
2.2022-2.25350.20332930.14995480X-RAY DIFFRACTION100
2.2535-2.30980.15022800.14775372X-RAY DIFFRACTION100
2.3098-2.37230.17312840.15185377X-RAY DIFFRACTION100
2.3723-2.44210.17162880.15275464X-RAY DIFFRACTION100
2.4421-2.52090.18282810.15255394X-RAY DIFFRACTION100
2.5209-2.61090.17932870.15525400X-RAY DIFFRACTION100
2.6109-2.71550.19322840.1535422X-RAY DIFFRACTION100
2.7155-2.8390.182860.16325393X-RAY DIFFRACTION100
2.839-2.98860.19412870.15795405X-RAY DIFFRACTION100
2.9886-3.17580.17582830.15165431X-RAY DIFFRACTION100
3.1758-3.42080.16582870.15385444X-RAY DIFFRACTION100
3.4208-3.76480.14692880.13675399X-RAY DIFFRACTION100
3.7648-4.30890.14372840.12865405X-RAY DIFFRACTION100
4.3089-5.42630.13882870.13025417X-RAY DIFFRACTION100
5.4263-37.98180.20242900.195375X-RAY DIFFRACTION100
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)
10.8998-0.12370.230.5488-0.16690.6653-0.00510.0440.0235-0.0358-0.0206-0.0902-0.04650.05390.02650.1132-0.01060.00970.0550.01350.077671.985-5.7425.3204
20.2486-0.22750.14351.5282-0.82780.94620.00860.0352-0.0149-0.07160.03980.1082-0.009-0.0726-0.04890.08990.00150.00050.0742-0.00360.068158.6893-16.5849-1.2781
30.5285-0.1152-0.24110.33330.09860.71460.0151-0.0037-0.0408-0.0069-0.0145-0.0020.00990.0159-0.00120.0783-0.00410.00540.0432-0.00090.07965.8771-19.408916.9627
41.01880.0495-0.06560.4959-0.14570.60140.0186-0.00930.06940.02360.01920.111-0.0691-0.1296-0.02860.10320.0120.01360.0668-0.00370.080351.03-6.067220.7596
51.1285-0.29030.08670.42720.04620.4592-0.0274-0.0245-0.05110.04680.0343-0.07530.08120.0906-0.00350.10380.0208-0.0070.08750.00010.095385.906-27.070923.3653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 107 through 189 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 190 through 337 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 440 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 441 through 654 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 655 through 793 )A0

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