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- PDB-1edq: CRYSTAL STRUCTURE OF CHITINASE A FROM S. MARCESCENS AT 1.55 ANGSTROMS -

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Basic information

Entry
Database: PDB / ID: 1edq
TitleCRYSTAL STRUCTURE OF CHITINASE A FROM S. MARCESCENS AT 1.55 ANGSTROMS
ComponentsCHITINASE A
KeywordsHYDROLASE / BETA-ALPHA (TIM) BARREL
Function / homology
Function and homology information


chitinase 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: 1.55 Å
AuthorsPapanikolau, Y. / Petratos, K.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: De 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.
#1: 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.
#2: 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.
History
DepositionJan 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 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: CHITINASE A


Theoretical massNumber of molelcules
Total (without water)58,6401
Polymers58,6401
Non-polymers00
Water16,376909
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.497, 131.825, 59.368
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: 58639.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O83008, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / 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: 3.3 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.75 M Citrate-Na pH 7.2, 20% (v/v) methanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mM1dropNaCl
2200 mMammonium sulfate1drop
330 mg/mlenzyme1drop
42 mMTris-HCl1drop
50.75 Msodium citrate1reservoir
620 %(v/v)methanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.55→10 Å / Num. all: 112857 / Num. obs: 112857 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 27.8
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.8 / Num. unique all: 11176 / % possible all: 100
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CTN

1ctn


Resolution: 1.55→10 Å / SU B: 1.328 / SU ML: 0.049 / σ(F): 0 / σ(I): 0 / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 5640 5 %RANDOM
Rwork0.187 ---
all0.188 112857 --
obs0.188 112857 99.8 %-
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 0 909 5129
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg1.2
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_plane_restr0.010.03
X-RAY DIFFRACTIONp_chiral_restr0.0930.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2410.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1960.3
X-RAY DIFFRACTIONp_planar_tor6.57
X-RAY DIFFRACTIONp_staggered_tor11.915
X-RAY DIFFRACTIONp_transverse_tor25.220
X-RAY DIFFRACTIONp_mcbond_it1.092
X-RAY DIFFRACTIONp_mcangle_it1.573
X-RAY DIFFRACTIONp_scbond_it1.52
X-RAY DIFFRACTIONp_scangle_it2.273
X-RAY DIFFRACTIONtorsion_deg11.9
X-RAY DIFFRACTIONpeptide_bond_planarity_d0.01
X-RAY DIFFRACTIONcontacts_van_der_waals_d0.24
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg11.9
X-RAY DIFFRACTIONp_mcbond_it1.092
X-RAY DIFFRACTIONp_scbond_it1.52
X-RAY DIFFRACTIONp_mcangle_it1.573
X-RAY DIFFRACTIONp_scangle_it2.273

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