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- PDB-2zux: Crystal structure of rhamnogalacturonan lyase YesW complexed with... -

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Basic information

Entry
Database: PDB / ID: 2zux
TitleCrystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose
ComponentsYesW proteinRhamnogalacturonan endolyase
KeywordsLYASE / Beta-propeller / Rhamnose complex
Function / homology
Function and homology information


rhamnogalacturonan endolyase / rhamnogalacturonan endolyase activity / cell wall organization / extracellular region / metal ion binding
Similarity search - Function
: / Rhamnogalacturonan lyase family 11, C-terminal domain / Polysaccharide lyase family 11 / Rhamnogalacturonan I lyase beta-sheet domain / Rhamnogalacturonan I lyases beta-sheet domain / Integrin alpha, N-terminal / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-rhamnopyranose / Rhamnogalacturonan endolyase YesW
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsOchiai, A. / Itoh, T. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases
Authors: Ochiai, A. / Itoh, T. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionOct 28, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YesW protein
B: YesW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,22731
Polymers129,0402
Non-polymers2,18729
Water22,6091255
1
A: YesW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,69616
Polymers64,5201
Non-polymers1,17615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YesW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,53215
Polymers64,5201
Non-polymers1,01114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.282, 105.858, 100.967
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YesW protein / Rhamnogalacturonan endolyase


Mass: 64520.133 Da / Num. of mol.: 2 / Fragment: UNP residues 38-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yesW, BSU07050 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: O31526, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose / Rhamnose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1255 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 55% MPD, 0.1M TRIS, pH8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 20, 2008 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 280440 / % possible obs: 97.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.8 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z8R

2z8r


Resolution: 1.32→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.667 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18033 13803 5 %RANDOM
Rwork0.16633 ---
obs0.16704 259908 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.536 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.52 Å2
2--0.74 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.32→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8954 0 97 1271 10322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0219255
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.94912552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49751166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31624.462437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.393151438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4491553
X-RAY DIFFRACTIONr_chiral_restr0.0790.21342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027179
X-RAY DIFFRACTIONr_nbd_refined0.1970.24393
X-RAY DIFFRACTIONr_nbtor_refined0.3070.26279
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0770.21079
X-RAY DIFFRACTIONr_metal_ion_refined0.1530.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.247
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0520.21
X-RAY DIFFRACTIONr_mcbond_it0.5471.55837
X-RAY DIFFRACTIONr_mcangle_it0.88229135
X-RAY DIFFRACTIONr_scbond_it1.32633925
X-RAY DIFFRACTIONr_scangle_it1.9154.53417
LS refinement shellResolution: 1.319→1.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 981 -
Rwork0.233 18169 -
obs--92.18 %

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