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- PDB-2z8s: Crystal structure of rhamnogalacturonan lyase YesW complexed with... -

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Basic information

Entry
Database: PDB / ID: 2z8s
TitleCrystal structure of rhamnogalacturonan lyase YesW complexed with digalacturonic acid
ComponentsYesW protein
KeywordsLYASE / BETA-PROPELLER
Function / homology
Function and homology information


rhamnogalacturonan endolyase / rhamnogalacturonan endolyase activity / cell wall organization / extracellular region / metal ion binding
Similarity search - Function
Polysaccharide lyase family 11 / Rhamnogalacturonan I lyase beta-sheet domain / : / Rhamnogalacturonan I lyases beta-sheet domain / Rhamnogalacturonan lyase family 11, C-terminal domain / Integrin alpha, N-terminal / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Rhamnogalacturonan endolyase YesW
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOchiai, A. / Itoh, T. / Maruyama, Y. / Kawamata, A. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER
Authors: Ochiai, A. / Itoh, T. / Maruyama, Y. / Kawamata, A. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionSep 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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)130,58224
Polymers129,0402
Non-polymers1,54222
Water6,035335
1
A: YesW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,29112
Polymers64,5201
Non-polymers77111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YesW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,29112
Polymers64,5201
Non-polymers77111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.617, 105.152, 100.668
Angle α, β, γ (deg.)90.00, 95.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 38 - 537 / Label seq-ID: 1 - 500

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein YesW protein


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 / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3)
References: UniProt: O31526, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Polysaccharide alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 370.263 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpAa1-4DGalpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112A-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GalpA]{[(4+1)][a-D-GalpA]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
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 293.0K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 21, 2007
RadiationMonochromator: Carbon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→26.2 Å / Num. obs: 37253 / % possible obs: 93.3 % / Redundancy: 1.53 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.059 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.14 % / Mean I/σ(I) obs: 2.41 / Rsym value: 0.233 / % possible all: 70

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SADIEdata collection
SAINTdata reduction
SAINTdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z8R

2z8r


Resolution: 2.5→26.15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.876 / SU B: 10.998 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24169 1708 5.1 %RANDOM
Rwork0.16157 ---
obs0.16568 31603 81.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8952 0 70 335 9357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219213
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.94912513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7151166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.524.495436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.502151435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8891552
X-RAY DIFFRACTIONr_chiral_restr0.0770.21323
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027190
X-RAY DIFFRACTIONr_nbd_refined0.2240.25596
X-RAY DIFFRACTIONr_nbtor_refined0.3150.26312
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2779
X-RAY DIFFRACTIONr_metal_ion_refined0.220.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.211
X-RAY DIFFRACTIONr_mcbond_it0.4151.55793
X-RAY DIFFRACTIONr_mcangle_it0.73429137
X-RAY DIFFRACTIONr_scbond_it0.89333881
X-RAY DIFFRACTIONr_scangle_it1.4344.53376
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3504 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.340.5
medium thermal0.452
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 77 -
Rwork0.268 1491 -
obs--52.87 %

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