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- PDB-1kr0: Hevamine Mutant D125A/Y183F in Complex with Tetra-NAG -

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Basic information

Entry
Database: PDB / ID: 1kr0
TitleHevamine Mutant D125A/Y183F in Complex with Tetra-NAG
ComponentsHevamine A
KeywordsHYDROLASE / chitinase/lysozyme
Function / homology
Function and homology information


chitinase / chitinase activity / vacuole / chitin catabolic process / polysaccharide catabolic process / lysozyme / lysozyme activity / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.92 Å
AuthorsRozeboom, H.J. / Dijkstra, B.W.
Citation
Journal: Eur.J.Biochem. / Year: 2002
Title: Expression and Characterization of Active Site Mutants of Hevamine, a Chitinase from the Rubber Tree Hevea brasiliensis.
Authors: Bokma, E. / Rozeboom, H.J. / Sibbald, M. / Dijkstra, B.W. / Beintema, J.J.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: The 1.8 A Resolution Structure of Hevamine, a Plant Chitinase/Lysozyme, and Analysis of the Conserved Sequence and Structure Motifs of Glycosyl Hydrolase Family 18.
Authors: Terwisscha van Scheltinga, A.C. / Hennig, M. / Dijkstra, B.W.
#2: Journal: Biochemistry / Year: 1995
Title: Stereochemistry of Chitin Hydrolysis by a Plant Chitinase/Lysozyme and X-ray Structure of a Complex with Allosamidin: Evidence for Substrate Assisted Catalysis.
Authors: Terwisscha van Scheltinga, A.C. / Armand, S. / Kalk, K.H. / Isogai, A. / Henrissat, B. / Dijkstra, B.W.
#3: Journal: Structure / Year: 1994
Title: Crystal Structures of Hevamine, a Plant Defence Protein with Chitinase and Lysozyme Activity, and its Complex with an Inhibitor.
Authors: Terwisscha van Scheltinga, A.C. / Kalk, K.H. / Beintema, J.J. / Dijkstra, B.W.
#4: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization of Hevamine, an Enzyme with Lysozyme/Chitinase Activity from Hevea brasiliensis Latex.
Authors: Rozeboom, H.J. / Budiani, A. / Beintema, J.J. / Dijkstra, B.W.
History
DepositionJan 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hevamine A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4403
Polymers29,5131
Non-polymers9272
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.945, 57.570, 82.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hevamine A


Mass: 29513.174 Da / Num. of mol.: 1 / Mutation: D125A/Y183F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Plasmid: pGELAF+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)trxB
References: UniProt: p23472, UniProt: P23472*PLUS, chitinase, lysozyme
#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.: 1
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 1.1-1.4 M / Common name: ammonium sulfate / Details: or 10-30%(w/v) PEG3350, pH7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 14, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 19371 / Num. obs: 19371 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.8
Reflection shellResolution: 1.92→1.95 Å / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 4.5 / Num. unique all: 927 / % possible all: 97.4
Reflection
*PLUS
Lowest resolution: 44 Å / Num. obs: 19419 / Num. measured all: 187850
Reflection shell
*PLUS
% possible obs: 97.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2HVM

2hvm


Resolution: 1.92→43.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1274359.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1001 5.2 %RANDOM
Rwork0.169 ---
all0.175 19328 --
obs0.175 19328 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.2003 Å2 / ksol: 0.352757 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.92→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 62 142 2287
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.62
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.92→1.99 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.247 93 5.2 %
Rwork0.212 1688 -
obs--93.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.2 % / Rfactor obs: 0.167 / Rfactor Rfree: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_mcangle_it1.62
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.247 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.212

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