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- PDB-6idn: Crystal structure of ICChI chitinase from ipomoea carnea -

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Basic information

Entry
Database: PDB / ID: 6idn
TitleCrystal structure of ICChI chitinase from ipomoea carnea
ComponentsICChI, a glycosylated chitinase
KeywordsPLANT PROTEIN / chitinase / glycosylation / TIM barrel / Ipomoea carnea
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / 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 speciesIpomoea carnea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKumar, S. / Kumar, A. / Patel, A.K.
CitationJournal: Phytochemistry / Year: 2020
Title: TIM barrel fold and glycan moieties in the structure of ICChI, a protein with chitinase and lysozyme activity.
Authors: Kumar, S. / Kumar, A. / Patel, A.K.
History
DepositionSep 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ICChI, a glycosylated chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2476
Polymers29,9991
Non-polymers2,2485
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint20 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.490, 59.490, 171.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein ICChI, a glycosylated chitinase


Mass: 29998.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ipomoea carnea (plant) / References: UniProt: A0A493R6X2*PLUS
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1026.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-2[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-5/a3-b1_a4-c1_c4-d1_d2-e1_d3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe authors submitted the sequence in GenBank Database (accession number: MH973622).

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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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5mM Cobalt Chloride, 5mM Cadmium Chloride, 5mM Magnesium Chloride, 5mM Nickle Chloride, 100mM HEPES pH 7.0, 11% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98401 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98401 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 50243 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 18.71 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 20.2
Reflection shellResolution: 1.5→3 Å / Rmerge(I) obs: 0.28 / Num. unique obs: 50372

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.13_2998refinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HVQ

1hvq


Resolution: 1.5→30 Å / SU ML: 0.1841 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.592
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 2521 5.02 %Random selection
Rwork0.1893 ---
obs0.191 50243 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 147 343 2609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652422
X-RAY DIFFRACTIONf_angle_d0.89593339
X-RAY DIFFRACTIONf_chiral_restr0.0574384
X-RAY DIFFRACTIONf_plane_restr0.0056421
X-RAY DIFFRACTIONf_dihedral_angle_d5.11281829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.331480.32922596X-RAY DIFFRACTION100
1.53-1.560.35971360.30952603X-RAY DIFFRACTION100
1.56-1.590.27871390.27162574X-RAY DIFFRACTION100
1.59-1.630.26961500.24632602X-RAY DIFFRACTION100
1.63-1.670.26641410.23222587X-RAY DIFFRACTION100
1.67-1.720.30111480.2312619X-RAY DIFFRACTION100
1.72-1.770.27451120.22352640X-RAY DIFFRACTION100
1.77-1.820.24341340.20732633X-RAY DIFFRACTION100
1.82-1.890.24831370.20572610X-RAY DIFFRACTION100
1.89-1.970.23591310.19142645X-RAY DIFFRACTION100
1.97-2.060.22351440.1972641X-RAY DIFFRACTION100
2.06-2.160.22331420.18142624X-RAY DIFFRACTION100
2.16-2.30.1921360.18152670X-RAY DIFFRACTION100
2.3-2.480.21621690.17982647X-RAY DIFFRACTION100
2.48-2.730.21021330.18082680X-RAY DIFFRACTION100
2.73-3.120.22111400.18352707X-RAY DIFFRACTION99.96
3.12-3.930.1921380.16682744X-RAY DIFFRACTION99.93
3.93-30.010.21481430.16912900X-RAY DIFFRACTION98.9
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)
11.77026331906-0.20571480898-0.4178362022131.86549845085-0.1360992519752.51456393359-0.2629352277870.161822466709-0.326184151835-0.2713436488480.1092085193880.008163074949910.770069698626-0.1018570000590.1442588053930.347053226207-0.03240157547970.01138465120830.114625429398-0.006724052823660.17789929814310.144740545622.892856029126.7767922274
20.55937946449-0.820072934216-0.7748800911332.327510154140.5711156609032.70915779357-0.4342622701340.0954051478742-0.383658029299-0.125302619570.220221563020.1306663328091.67577388678-0.6641821359290.2946696916910.692767962525-0.08105336122170.06863429497860.138971945246-0.01357076103730.2460552012246.2795048699515.692604563131.9110101864
32.15113195132-0.318697516466-0.4815612177573.16501472274-0.6246874128133.22442939579-0.02415453830510.0181383780597-0.0190742726042-0.1324857301950.09281806007440.1760893345290.283456358392-0.350728608436-0.07955570095990.135594683942-0.0169234554513-0.01861795135560.1246273926140.005754722924320.1220909538163.9089378004627.246879366540.1370535339
41.477244366630.639576295490.2954961137642.34340052993-0.5662701175954.13759347174-0.066216042136-0.0403533158350.00598893041897-0.01572526584340.04932677038120.07449140186930.179332806885-0.1870466951890.02465558575350.0902209901181-0.000819069595310.01579750180420.09836307345720.0001394309506710.123371847567.9333533073132.461714146740.1785495868
52.072230147071.3043591514-1.044004257091.242060947070.7611285898344.3842010264-0.059089707946-0.002127075758460.15724818172-0.05498263401740.08589217538230.0569862197355-0.222734258527-0.2724829917510.0001724186591930.114325746280.0193271595520.007104426663450.098968730282-0.01076945843870.1503961872469.3894963246539.311171421131.9541785704
60.5509326315010.414279277883-0.1664989169060.177499820817-0.2359942035239.03853889967-0.01280335875490.08394152239480.0650687613017-0.01125156443430.08084037442460.112861114485-0.0981637026554-0.370995833756-0.04228473719720.1067322279820.00222543089396-0.007294414812550.1078992868140.0141517396740.17120458186211.583645461641.304148323324.5678993052
71.31353679480.4774439319820.4716026570452.146849612840.4063298966924.86675016346-0.1141567072130.1650230241710.0611636831175-0.09487127893730.09202881111890.0751486311062-0.190032316104-0.0105501801165-0.004361616518910.103566523915-0.02154999283610.001091620163730.1175600555030.01287367085450.12773108907515.546278586140.769280221919.9472686172
81.056865251740.5623854859130.3954493014252.202434832060.452989980035.85381055637-0.08723294072180.1733252853650.0123762174376-0.06637901829090.169059857767-0.2284901452640.026999259030.568544713788-0.08069832647930.1018720552420.01173448760220.01418659902470.162529871291-0.01220497905080.15690931036822.11909987637.275168961218.3396617447
99.155470587971.82142639389-1.255682982314.49131495077-0.1659233789314.2918492397-0.09668615098460.406122737214-0.715117854517-0.3549331245060.0742771316148-0.2982966176590.9394518476660.1014327724430.03767454002580.3639727206470.02907035727970.02856493150810.162493278479-0.02473655430750.17155044790617.685874543125.421320279814.7528191871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 114 )
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 148 )
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 167 )
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 195 )
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 232 )
8X-RAY DIFFRACTION8chain 'A' and (resid 233 through 256 )
9X-RAY DIFFRACTION9chain 'A' and (resid 257 through 272 )

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