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- PDB-1ffr: CRYSTAL STRUCTURE OF CHITINASE A MUTANT Y390F COMPLEXED WITH HEXA... -

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Basic information

Entry
Database: PDB / ID: 1ffr
TitleCRYSTAL STRUCTURE OF CHITINASE A MUTANT Y390F COMPLEXED WITH HEXA-N-ACETYLCHITOHEXAOSE (NAG)6
ComponentsCHITINASE A
KeywordsHYDROLASE / TIM BARREL / PROTEIN-OLIGOSACCHARIDE COMPLEX
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II ...Chitinase A N-terminal / Chitinase A, N-terminal domain / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPapanikolau, Y. / Prag, G. / Tavlas, G. / Vorgias, C.E. / Oppenheim, A.B. / Petratos, K.
Citation
Journal: Biochemistry / Year: 2001
Title: High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis.
Authors: Papanikolau, Y. / Prag, G. / Tavlas, G. / Vorgias, C.E. / Oppenheim, A.B. / Petratos, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: CDE NOVO PURIFICATION SCHEME AND CRYSTALLIZATION CONDITIONS YIELD HIGH-RESOLUTION STRUCTURES OF CHITINASE A AND ITS COMPLEX WITH THE INHIBITOR ALLOSAMIDIN
Authors: Papanikolau, Y. / Tavlas, G. / Vorgias, C.E. / Petratos, K.
#2: Journal: Structure / Year: 1994
Title: Crystal Structure of a bacterial chitinase at 2.3 Angstrom resolution
Authors: Perrakis, A. / Tews, I. / Dauter, Z. / Oppenheim, A.B. / Chet, I. / Wilson, K.S. / Vorgias, C.E.
History
DepositionJul 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 14, 2018Group: Data collection / Database references / Category: diffrn_source / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_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 / _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 2.1Aug 9, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHITINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0642
Polymers58,6241
Non-polymers1,4401
Water13,926773
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.172, 131.921, 59.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CHITINASE A


Mass: 58623.590 Da / Num. of mol.: 1 / Mutation: Y390F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: 2170 / Plasmid: PBR322 / Production host: Escherichia coli (E. coli)
References: GenBank: AB015996, UniProt: P07254*PLUS, 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-(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: 1440.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 3.25 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.75 M CITRATE-NA AND 20% (V/V) METHANOL, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 18-20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
20.75 Msodium citrate1reservoir
320 %(v/v)methanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 17, 2000 / Details: PAIR OF NICKEL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 68036 / Num. obs: 68036 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.4
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 6.2 / Num. unique all: 6945 / % possible all: 96.8
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 96.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.18

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EDQ

1edq


Resolution: 1.8→10 Å / SU B: 2.39 / SU ML: 0.08 / σ(F): 0 / σ(I): 0 / ESU R: 0.12 / ESU R Free: 0.12 / Stereochemistry target values: Engh & Huber
Details: THE CLOSE CONTACT LISTED IN REMARK 500 IS DUE TO THE RESULT OF AVERAGING OF TWO CO-EXISTING STRUCTURES WITH UNCLEAVED AND CLEAVED BOND BETWEEN ATOMS O4 AND C1 OF THE SUGAR RESIDUES
RfactorNum. reflectionSelection details
Rfree0.229 3453 RANDOM
Rwork0.183 --
all0.186 68015 -
obs0.186 68015 -
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 99 773 5008
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONn_plane_restr0.0120.03
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.1860.3
X-RAY DIFFRACTIONp_multtor_nbd0.280.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.230.3
X-RAY DIFFRACTIONp_planar_tor6.57
X-RAY DIFFRACTIONp_staggered_tor13.615
X-RAY DIFFRACTIONp_transverse_tor25.920
X-RAY DIFFRACTIONp_mcbond_it1.422
X-RAY DIFFRACTIONp_mcangle_it1.973
X-RAY DIFFRACTIONp_scbond_it1.812
X-RAY DIFFRACTIONp_scangle_it2.733
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_mcbond_it1.422
X-RAY DIFFRACTIONp_scbond_it1.812
X-RAY DIFFRACTIONp_mcangle_it1.973
X-RAY DIFFRACTIONp_scangle_it2.733

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