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- PDB-5uas: Structure of a new family of Polysaccharide lyase PL25-Ulvanlyase... -

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Basic information

Entry
Database: PDB / ID: 5uas
TitleStructure of a new family of Polysaccharide lyase PL25-Ulvanlyase bound to -[GlcA(1-4)Rha3S]-
ComponentsUlvanLyase-PL25
KeywordsLYASE / Beta propellar fold / degrades Ulvan polysaccharide
Function / homologyBNR repeat-containing family member / Lyases; Carbon-oxygen lyases; Acting on polysaccharides / Sialidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / lyase activity / metal ion binding / plasma membrane / : / Ulvan Lyase-PL25
Function and homology information
Biological speciesPseudoalteromonas sp. PLSV (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsUlaganathan, T.S. / Cygler, M.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture.
Authors: Ulaganathan, T. / Boniecki, M.T. / Foran, E. / Buravenkov, V. / Mizrachi, N. / Banin, E. / Helbert, W. / Cygler, M.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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.mon_nstd_flag / _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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UlvanLyase-PL25
B: UlvanLyase-PL25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,34315
Polymers106,1432
Non-polymers2,20013
Water20,3211128
1
A: UlvanLyase-PL25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2028
Polymers53,0721
Non-polymers1,1317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UlvanLyase-PL25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1407
Polymers53,0721
Non-polymers1,0696
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.620, 71.810, 109.270
Angle α, β, γ (deg.)90.00, 122.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein UlvanLyase-PL25


Mass: 53071.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas sp. PLSV (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W2VMZ5*PLUS
#2: Polysaccharide 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose-(1-4)-beta-D- ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 804.657 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2211m-1a_1-5_3*OSO/3=O/3=O][a2122A-1b_1-5][a21eEA-1a_1-5]/1-2-1-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap3SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-L-Rhap3SO3]{[(4+1)][a-L-4-deoxy-IdopA]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1139 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1128 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 15% PEG3500, 0.2M ammonium acetate, 0.1M Bis-Tris pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9871 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9871 Å / Relative weight: 1
ReflectionResolution: 1.6→47.8 Å / Num. obs: 143590 / % possible obs: 95.4 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.75

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UAM
Resolution: 1.6→47.8 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.99
RfactorNum. reflection% reflection
Rfree0.212 7181 5 %
Rwork0.182 --
obs0.183 143590 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6937 0 130 1128 8195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097281
X-RAY DIFFRACTIONf_angle_d1.1229872
X-RAY DIFFRACTIONf_dihedral_angle_d14.0544201
X-RAY DIFFRACTIONf_chiral_restr0.1351017
X-RAY DIFFRACTIONf_plane_restr0.0071295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61820.40812010.32283839X-RAY DIFFRACTION82
1.6182-1.63720.36932330.3184425X-RAY DIFFRACTION93
1.6372-1.65720.34242360.27674480X-RAY DIFFRACTION95
1.6572-1.67820.30782370.26744503X-RAY DIFFRACTION96
1.6782-1.70020.30752360.25624477X-RAY DIFFRACTION96
1.7002-1.72350.27992370.24824509X-RAY DIFFRACTION96
1.7235-1.74820.26122390.22594523X-RAY DIFFRACTION96
1.7482-1.77430.25832400.20574573X-RAY DIFFRACTION96
1.7743-1.8020.2392380.2044512X-RAY DIFFRACTION96
1.802-1.83150.22732380.19494533X-RAY DIFFRACTION96
1.8315-1.86310.24662390.20474525X-RAY DIFFRACTION96
1.8631-1.8970.25442400.22744559X-RAY DIFFRACTION96
1.897-1.93350.32632350.28764459X-RAY DIFFRACTION95
1.9335-1.97290.22972410.21324585X-RAY DIFFRACTION97
1.9729-2.01580.20212400.18024568X-RAY DIFFRACTION97
2.0158-2.06270.19332410.18824572X-RAY DIFFRACTION97
2.0627-2.11430.24232400.20144567X-RAY DIFFRACTION97
2.1143-2.17150.21172420.17024596X-RAY DIFFRACTION97
2.1715-2.23540.2312430.17824615X-RAY DIFFRACTION97
2.2354-2.30750.21172380.1934519X-RAY DIFFRACTION96
2.3075-2.390.18012420.16794588X-RAY DIFFRACTION97
2.39-2.48570.20412420.17064603X-RAY DIFFRACTION97
2.4857-2.59880.21862410.16364575X-RAY DIFFRACTION97
2.5988-2.73580.19752420.16824605X-RAY DIFFRACTION97
2.7358-2.90720.19222410.16844578X-RAY DIFFRACTION97
2.9072-3.13160.20072450.16344641X-RAY DIFFRACTION97
3.1316-3.44670.18742440.15764652X-RAY DIFFRACTION98
3.4467-3.94520.18192460.15294667X-RAY DIFFRACTION98
3.9452-4.96980.17182480.13884702X-RAY DIFFRACTION98
4.9698-47.82940.1912560.18424859X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.82240.23670.02350.88990.32221.2056-0.0011-0.04350.03840.0538-0.01660.093-0.0215-0.14150.00680.11460.00750.0030.13550.01360.1396-0.590280.167338.8157
21.08010.1889-0.17071.020.22070.87470.0086-0.11150.00810.06550.0915-0.0345-0.0730.1235-0.1010.1291-0.0057-0.00560.1148-0.0140.105115.258785.89241.9911
30.92490.2609-0.09830.98750.75031.22940.00660.1153-0.0245-0.18690.1768-0.238-0.25770.3224-0.07950.1697-0.06060.05180.1788-0.05050.128623.158582.375222.21
41.66510.2902-0.18980.87970.33571.2515-0.00560.2196-0.1827-0.13960.02180.04130.036-0.0231-0.01010.14950.0063-0.01060.1575-0.02480.12539.000471.2516.9098
51.5669-0.7666-0.40251.30020.50870.53670.03160.2378-0.2742-0.0673-0.12090.20320.1146-0.10610.09770.1433-0.0098-0.03080.1825-0.03660.17150.816567.529919.6481
61.1830.3357-0.0140.9595-0.34431.1477-0.0193-0.016-0.03670.0438-0.00320.15640.058-0.14630.02040.1237-0.00680.00160.1549-0.01230.1502-4.096372.828835.1309
71.0916-0.41510.30651.1174-0.2021.19030.02090.08210.0373-0.13460.0158-0.2204-0.04310.1609-0.03020.1321-0.01430.02620.1428-0.0280.175256.814744.2675.7223
81.0427-0.465-0.06330.99260.23810.83410.02040.08660.0864-0.12450.0578-0.051-0.1011-0.058-0.07180.1647-0.0056-0.00590.12910.01740.13942.383551.47154.9738
91.7864-0.6760.13991.4011-0.33651.2849-0.1011-0.42070.03630.22950.15570.0536-0.1032-0.2363-0.04090.15960.04290.00290.23910.0060.119337.616945.953126.214
101.70180.1867-0.29461.3206-0.4921.0937-0.0893-0.314-0.29750.16420.13-0.0920.1204-0.0072-0.0330.1430.0138-0.0280.21470.0340.194455.583732.602126.468
111.2864-0.35760.32821.00210.62451.22380.05480.0396-0.1289-0.07490.0583-0.30780.0630.165-0.08520.1251-0.00280.01610.166-0.02460.214462.285537.27469.7971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 47 THROUGH 126)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 127 THROUGH 227 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 228 THROUGH 348 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 349 THROUGH 416 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 417 THROUGH 439 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 440 THROUGH 486 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 48 THROUGH 135 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 136 THROUGH 227 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 228 THROUGH 376)
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 377 THROUGH 439 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 440 THROUGH 487 )

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