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- PDB-3b9e: Crystal structure of inactive mutant E315M chitinase A from Vibri... -

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Basic information

Entry
Database: PDB / ID: 3b9e
TitleCrystal structure of inactive mutant E315M chitinase A from Vibrio harveyi
ComponentsChitinase A
KeywordsHYDROLASE / TIM-barrel / Glycosidase
Function / homology
Function and homology information


chitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Chitinase A N-terminal / Chitinase A, N-terminal domain / K319L-like, PKD domain / PKD domain / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / PKD domain / PKD domain superfamily / PKD/Chitinase domain ...Chitinase A N-terminal / Chitinase A, N-terminal domain / K319L-like, PKD domain / PKD domain / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / PKD domain / PKD domain superfamily / 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 speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSongsiriritthigul, C. / Pantoom, S. / Aguda, A.H. / Robinson, R.C. / Suginta, W.
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Crystal structures of Vibrio harveyi chitinase A complexed with chitooligosaccharides: implications for the catalytic mechanism
Authors: Songsiriritthigul, C. / Pantoom, S. / Aguda, A.H. / Robinson, R.C. / Suginta, W.
History
DepositionNov 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.5Oct 16, 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


Theoretical massNumber of molelcules
Total (without water)63,8441
Polymers63,8441
Non-polymers00
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.960, 83.106, 106.980
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 Chitinase A / endochitinase A / Glycosylhydrolase / Family 18 chitinase


Mass: 63843.855 Da / Num. of mol.: 1 / Mutation: E315M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Strain: LMG7890
Description: VIBRIO HARVEYI was called formerly Vibrio carchariae
Gene: CHIA / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9AMP1, chitinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 4000, 0.1M ammonium sulfate, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→24.68 Å / Num. all: 61563 / Num. obs: 61563 / % possible obs: 97.2 % / Redundancy: 9.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.075 / Net I/σ(I): 26.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 4.5 / Num. unique all: 7880 / Rsym value: 0.387 / % possible all: 87.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CTN

1ctn


Resolution: 1.7→24.68 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.106 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 3118 5.1 %RANDOM
Rwork0.18898 ---
all0.1905 61563 --
obs0.1905 58390 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.603 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4474 0 0 740 5214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224597
X-RAY DIFFRACTIONr_angle_refined_deg0.9321.9386252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0925579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33825.023215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11115699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.991513
X-RAY DIFFRACTIONr_chiral_restr0.0670.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023604
X-RAY DIFFRACTIONr_nbd_refined0.1750.22306
X-RAY DIFFRACTIONr_nbtor_refined0.30.23126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0810.2616
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.245
X-RAY DIFFRACTIONr_mcbond_it0.4451.52937
X-RAY DIFFRACTIONr_mcangle_it0.61724584
X-RAY DIFFRACTIONr_scbond_it0.94731947
X-RAY DIFFRACTIONr_scangle_it1.3444.51668
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 188 -
Rwork0.317 3427 -
obs-3427 78.57 %

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