[English] 日本語
Yorodumi
- PDB-4f13: Alginate lyase A1-III Y246F complexed with tetrasaccharide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f13
TitleAlginate lyase A1-III Y246F complexed with tetrasaccharide
ComponentsAlginate lyase
KeywordsLYASE / ALPHA BARREL / POLYSACCHARIDE LYASE / Alginate
Function / homology
Function and homology information


periplasmic space / lyase activity
Similarity search - Function
Alginate lyase domain / Alginate lyase / Alginate lyase 2 / Alginate lyase / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Glycosyltransferase / Alpha/alpha barrel / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSphingomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.208 Å
AuthorsMikami, B. / Ban, M. / Suzuki, S. / Yoon, H.-J. / Miyake, O. / Yamasaki, M. / Ogura, K. / Maruyama, Y. / Hashimoto, W. / Murata, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III
Authors: Mikami, B. / Ban, M. / Suzuki, S. / Yoon, H.-J. / Miyake, O. / Yamasaki, M. / Ogura, K. / Maruyama, Y. / Hashimoto, W. / Murata, K.
History
DepositionMay 6, 2012Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 27, 2012ID: 4E25
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
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 / struct_asym / struct_conn / 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.occupancy / _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 / _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.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 2.1Nov 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,7124
Polymers79,6382
Non-polymers1,0752
Water4,846269
1
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5232
Polymers39,8191
Non-polymers7041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1892
Polymers39,8191
Non-polymers3701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.571, 77.560, 145.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A5 - 9
121CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A11 - 13
131CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A15 - 31
141CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A35 - 60
151CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A86 - 157
161CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A159 - 168
171CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A170 - 208
181CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A212 - 296
191CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A298 - 352
211CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B5 - 9
221CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B11 - 13
231CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B15 - 31
241CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B35 - 60
251CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B86 - 157
261CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B159 - 168
271CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B170 - 208
281CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B212 - 296
291CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B298 - 352
112CHAIN A AND (RESSEQ 402:403 )A402 - 403
212CHAIN B AND (RESSEQ 401:402 )B401 - 413

NCS ensembles :
ID
1
2

-
Components

#1: Protein Alginate lyase / ALGINATE LYASE A1-III


Mass: 39818.773 Da / Num. of mol.: 2 / Fragment: UNP residues 54-404 / Mutation: Y246F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas (bacteria) / Strain: A1 / Gene: aly / Plasmid: PISA412 / Production host: BACILLUS SUBTILIS (bacteria)
References: UniProt: Q9KWU1, mannuronate-specific alginate lyase
#2: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 704.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a1122A-1b_1-5][a11eEA-1a_1-5]/1-1-1-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][a-L-4-deoxy-AllpA]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 370.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122A-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24%(W/V) PEG4000, 0.3M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.733 Å / Num. all: 37971 / Num. obs: 36529 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 5.39 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 16.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3 / Num. unique all: 3249 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4E1Y

4e1y


Resolution: 2.208→48.733 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8397 / SU ML: 0.25 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1835 5.03 %RANDOM
Rwork0.1771 ---
obs0.179 36472 95.85 %-
all-38051 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.015 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 120.02 Å2 / Biso mean: 31.0681 Å2 / Biso min: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.7695 Å20 Å20 Å2
2--1.3412 Å20 Å2
3---1.4283 Å2
Refine analyzeLuzzati coordinate error obs: 2.3 Å / Luzzati d res low obs: 4 Å
Refinement stepCycle: LAST / Resolution: 2.208→48.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5555 0 73 269 5897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015871
X-RAY DIFFRACTIONf_angle_d1.3057991
X-RAY DIFFRACTIONf_chiral_restr0.085857
X-RAY DIFFRACTIONf_plane_restr0.0061045
X-RAY DIFFRACTIONf_dihedral_angle_d19.5552216
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2424X-RAY DIFFRACTIONPOSITIONAL0.082
12B2424X-RAY DIFFRACTIONPOSITIONAL0.082
21A24X-RAY DIFFRACTIONPOSITIONAL0.2
22B24X-RAY DIFFRACTIONPOSITIONAL0.2
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2084-2.26810.32731310.24822472260391
2.2681-2.33480.30381320.23552591272395
2.3348-2.41020.30651340.22982615274995
2.4102-2.49630.22351360.22152624276095
2.4963-2.59630.31351530.2132576272995
2.5963-2.71440.23131220.21732627274995
2.7144-2.85750.28121450.21342612275795
2.8575-3.03650.24021380.19362624276296
3.0365-3.27090.21441450.18642655280095
3.2709-3.60.21061230.16712693281696
3.6-4.12070.17541570.13952757291498
4.1207-5.19070.15151610.132728182979100
5.1907-48.74510.17921580.156129733131100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more