[English] 日本語
Yorodumi
- PDB-4f10: Alginate lyase A1-III H192A complexed with tetrasaccharide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f10
TitleAlginate lyase A1-III H192A complexed with tetrasaccharide
ComponentsAlginate lyase
KeywordsLYASE / ALPHA BARREL / polysaccharide LYASE / Aliginate
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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 5, 2012Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 27, 2012ID: 4E23
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 / _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)80,6104
Polymers79,5352
Non-polymers1,0752
Water5,152286
1
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4722
Polymers39,7681
Non-polymers7041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1382
Polymers39,7681
Non-polymers3701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.386, 77.607, 145.411
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 - 32
141CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A35 - 63
151CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A86 - 92
161CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A94 - 210
171CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A212 - 289
181CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A291 - 295
191CHAIN A AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...A297 - 354
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 - 32
241CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B35 - 63
251CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B86 - 92
261CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B94 - 210
271CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B212 - 289
281CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B291 - 295
291CHAIN B AND (RESSEQ 5:9 OR RESSEQ 11:13 OR RESSEQ...B297 - 354
112CHAIN A AND (RESSEQ 402:403 )A402 - 403
212CHAIN B AND (RESSEQ 401:402 )B401 - 402

NCS ensembles :
ID
1
2

-
Components

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


Mass: 39767.703 Da / Num. of mol.: 2 / Fragment: UNP residues 54-404 / Mutation: H192A
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)-alpha-L-gulopyranuronic acid-(1-4)-beta-D- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic 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=2.0/3,4,3/[a1122A-1b_1-5][a1121A-1a_1-5][a11eEA-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-4-deoxy-AllpA]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-gulopyranuronic 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
LGulpAa1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122A-1b_1-5][a1121A-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][a-L-GulpA]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
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: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Feb 9, 2001 / Details: CARBON MONOCLOMETER
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→41.2 Å / Num. all: 38452 / Num. obs: 38230 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.089 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.86 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 3686 / Rsym value: 0.367 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
FRAMBOdata collection
CNSrefinement
PHENIX(phenix.refine: 1.6.4_486)refinement
SAINTdata reduction
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3EVH

3evh
PDB Unreleased entry


Resolution: 2.2→41.2 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8188 / SU ML: 0.19 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1913 5.01 %RANDOM
Rwork0.194 ---
obs0.1963 38167 99.53 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.965 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 98.34 Å2 / Biso mean: 25.2084 Å2 / Biso min: 3.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.636 Å20 Å2-0 Å2
2--3.7607 Å2-0 Å2
3----3.1247 Å2
Refine analyzeLuzzati coordinate error obs: 2.1 Å / Luzzati d res low obs: 4 Å
Refinement stepCycle: LAST / Resolution: 2.2→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5499 0 73 286 5858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135788
X-RAY DIFFRACTIONf_angle_d1.3697874
X-RAY DIFFRACTIONf_chiral_restr0.084850
X-RAY DIFFRACTIONf_plane_restr0.0051026
X-RAY DIFFRACTIONf_dihedral_angle_d18.6412172
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2480X-RAY DIFFRACTIONPOSITIONAL0.153
12B2480X-RAY DIFFRACTIONPOSITIONAL0.153
21A24X-RAY DIFFRACTIONPOSITIONAL0.237
22B24X-RAY DIFFRACTIONPOSITIONAL0.237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2550.34751290.31832501263097
2.255-2.3160.3041430.28972503264699
2.316-2.38410.33971450.2682509265499
2.3841-2.46110.33641380.26952555269399
2.4611-2.5490.33251300.25322550268099
2.549-2.65110.29821290.235225712700100
2.6511-2.77170.28971200.231226072727100
2.7717-2.91780.26681470.200825722719100
2.9178-3.10050.2371370.190526102747100
3.1005-3.33980.21351400.176625722712100
3.3398-3.67580.20061280.162826232751100
3.6758-4.20720.18731390.144126332772100
4.2072-5.29880.17391330.133926592792100
5.2988-41.20760.18991550.157927892944100

+
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://pdbjlvh1.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