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- PDB-4pxv: Crystal Structure of LysM domain from pteris ryukyuensis chitinase A -

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Basic information

Entry
Database: PDB / ID: 4pxv
TitleCrystal Structure of LysM domain from pteris ryukyuensis chitinase A
ComponentsChitinase A
KeywordsSUGAR BINDING PROTEIN / LysM domain / carbohydrate-binding module / Chitinase / carbohydrate
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Chitinase-like / Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / Lysin motif / LysM domain superfamily / LysM domain profile. / LysM domain / LysM domain / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. ...Chitinase-like / Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / Lysin motif / LysM domain superfamily / LysM domain profile. / LysM domain / LysM domain / 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 / Glycoside hydrolase superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesPteris ryukyuensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsOhnuma, T. / Umemoto, N. / Numata, T. / Fukamizo, T.
CitationJournal: To be Published
Title: Crystal Structure of LysM domain from pteris ryukyuensis chitinase A
Authors: Ohnuma, T. / Numata, T. / Taira, T. / Fukamizo, T.
History
DepositionMar 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.pdbx_dist_value / _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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitinase A
B: Chitinase A
C: Chitinase A
D: Chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4458
Polymers21,1844
Non-polymers2624
Water2,972165
1
A: Chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4273
Polymers5,2961
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3612
Polymers5,2961
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chitinase A


Theoretical massNumber of molelcules
Total (without water)5,2961
Polymers5,2961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chitinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3612
Polymers5,2961
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.686, 50.229, 92.292
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/peptide
Chitinase A


Mass: 5295.958 Da / Num. of mol.: 4 / Fragment: LysM domain, UNP RESIDUES 88-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pteris ryukyuensis (plant) / Gene: prchiA / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0WYK2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05M zinc acetate dihydrate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.28213 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 4, 2013
RadiationMonochromator: Numerical link type Si(111) double monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28213 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17318 / % possible obs: 99.9 % / Redundancy: 14 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 69.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 20 / Num. unique all: 11551 / % possible all: 9.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→46.15 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.488 / SU ML: 0.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22908 873 5.1 %RANDOM
Rwork0.19138 ---
obs0.19322 16397 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å2-0 Å20 Å2
2--0.19 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 4 165 1550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021408
X-RAY DIFFRACTIONr_bond_other_d0.0010.021247
X-RAY DIFFRACTIONr_angle_refined_deg1.0721.9191923
X-RAY DIFFRACTIONr_angle_other_deg0.73432861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0885185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08125.86258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13215208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.776154
X-RAY DIFFRACTIONr_chiral_restr0.0660.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021655
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02321
X-RAY DIFFRACTIONr_mcbond_it0.7221.38752
X-RAY DIFFRACTIONr_mcbond_other0.7231.379751
X-RAY DIFFRACTIONr_mcangle_it1.2692.058933
X-RAY DIFFRACTIONr_mcangle_other1.2682.059934
X-RAY DIFFRACTIONr_scbond_it0.8531.44656
X-RAY DIFFRACTIONr_scbond_other0.8521.439655
X-RAY DIFFRACTIONr_scangle_other1.3862.132990
X-RAY DIFFRACTIONr_long_range_B_refined3.62311.6181769
X-RAY DIFFRACTIONr_long_range_B_other3.28811.1981699
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 53 -
Rwork0.221 1204 -
obs--99.29 %

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