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- PDB-4yza: C. bescii Family 3 pectate lyase double mutant K108A/Q111A in com... -

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Basic information

Entry
Database: PDB / ID: 4yza
TitleC. bescii Family 3 pectate lyase double mutant K108A/Q111A in complex with trigalacturonic acid
ComponentsPectate lyase
KeywordsLYASE / PL3 / PARALLEL BETA-HELIX
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / hydrolase activity / extracellular region / metal ion binding / membrane
Similarity search - Function
Pectate lyase PlyH/PlyE-like / Pectate lyase / 3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
alpha-D-galactopyranuronic acid / beta-D-galactopyranuronic acid / IMIDAZOLE / pectate lyase
Similarity search - Component
Biological speciesCaldicellulosiruptor bescii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.
Authors: Alahuhta, M. / Taylor, L.E. / Brunecky, R. / Sammond, D.W. / Michener, W. / Adams, M.W. / Himmel, M.E. / Bomble, Y.J. / Lunin, V.
History
DepositionMar 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_alt_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_alt_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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 25, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
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_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pectate lyase
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,95828
Polymers44,0982
Non-polymers3,86126
Water11,007611
1
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,38417
Polymers22,0491
Non-polymers2,33516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,57411
Polymers22,0491
Non-polymers1,52510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.820, 36.430, 100.520
Angle α, β, γ (deg.)90.00, 132.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-439-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pectate lyase


Mass: 22048.857 Da / Num. of mol.: 2 / Mutation: K375A, Q378A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320) (bacteria)
Strain: ATCC BAA-1888 / DSM 6725 / Z-1320 / Gene: Athe_1854 / Production host: Escherichia coli (E. coli) / References: UniProt: B9MKT4, pectate lyase

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Sugars , 4 types, 11 molecules

#2: Polysaccharide alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-talopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpAa1-4DGalpAa1-4DTalpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1112A-1a_1-5][a2112A-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
#3: Polysaccharide alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpAa1-4DGalpAa1-4DGalpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2112A-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-ADA / alpha-D-galactopyranuronic acid / alpha-D-galacturonic acid / D-galacturonic acid / galacturonic acid / ALPHA D-GALACTURONIC ACID


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 626 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 9 and 65.9% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98397 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98397 Å / Relative weight: 1
ReflectionResolution: 1.25→50.89 Å / Num. obs: 100777 / % possible obs: 98.5 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 25.6
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 2.3 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPphasing
XDSdata reduction
XSCALEdata scaling
RefinementResolution: 1.25→50.89 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.523 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.151 4803 4.8 %RANDOM
Rwork0.108 ---
obs0.11 95973 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.25→50.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 239 611 3822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023689
X-RAY DIFFRACTIONr_bond_other_d0.0010.023447
X-RAY DIFFRACTIONr_angle_refined_deg2.14525083
X-RAY DIFFRACTIONr_angle_other_deg0.9563.0218025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0175479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51727.315149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04315611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.133152
X-RAY DIFFRACTIONr_chiral_restr0.1260.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024278
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02778
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8851.0921811
X-RAY DIFFRACTIONr_mcbond_other1.88444.8461810
X-RAY DIFFRACTIONr_mcangle_it2.3381.6472325
X-RAY DIFFRACTIONr_mcangle_other2.3417.4682326
X-RAY DIFFRACTIONr_scbond_it4.081.4681878
X-RAY DIFFRACTIONr_scbond_other4.082.5531879
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5088.3852759
X-RAY DIFFRACTIONr_long_range_B_refined4.7084540
X-RAY DIFFRACTIONr_long_range_B_other4.0694154
X-RAY DIFFRACTIONr_rigid_bond_restr7.10433689
X-RAY DIFFRACTIONr_sphericity_free18.812521
X-RAY DIFFRACTIONr_sphericity_bonded12.54553779
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 333 -
Rwork0.261 6792 -
obs--94.84 %

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