[English] 日本語
Yorodumi
- PDB-6jpn: Crystal structure of the catalytic domain of a multi-domain algin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jpn
TitleCrystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila
ComponentsAlginate lyase
KeywordsLYASE / alpha barrel+beta sandwich
Function / homology
Function and homology information


mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / hydrolase activity, acting on glycosyl bonds / metabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Heparinase II/III-like / Heparinase II/III-like protein / Alginate lyase / Chondroitin AC/alginate lyase / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain ...Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Heparinase II/III-like / Heparinase II/III-like protein / Alginate lyase / Chondroitin AC/alginate lyase / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesDefluviitalea phaphyphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.85 Å
AuthorsJi, S.Q. / Dix, S.R. / Aziz, A. / Sedelnikova, S.E. / Li, F.L. / Rice, D.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670001 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The molecular basis of endolytic activity of a multidomain alginate lyase fromDefluviitalea phaphyphila, a representative of a new lyase family, PL39.
Authors: Ji, S. / Dix, S.R. / Aziz, A.A. / Sedelnikova, S.E. / Baker, P.J. / Rafferty, J.B. / Bullough, P.A. / Tzokov, S.B. / Agirre, J. / Li, F.L. / Rice, D.W.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4296
Polymers88,3711
Non-polymers1,0585
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.380, 261.380, 58.450
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Alginate lyase


Mass: 88370.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Defluviitalea phaphyphila (bacteria) / References: UniProt: A0A4Y5UXE1*PLUS
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 898.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122A-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 41 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalMosaicity: 0.141 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5 / Details: 15% PEG 6000, 0.1 M magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.85→226.36 Å / Num. obs: 53459 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 67.276 Å2 / Rpim(I) all: 0.072 / Rrim(I) all: 0.238 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all
2.85-2.99.8126680.6482.036
7.73-62.810.739.227960.0170.056

-
Phasing

Phasing
Method
SAD
molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
xia2data scaling
PHASERphasing
SHELXphasing
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.85→62.86 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.176 / SU B: 14.232 / SU ML: 0.223 / Average fsc free: 0.8027 / Average fsc work: 0.8027 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.229
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 2701 5.053 %RANDOM
Rwork0.2071 50756 --
all0.208 ---
obs-53457 99.936 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 68.494 Å2
Baniso -1Baniso -2Baniso -3
1--3.895 Å2-1.947 Å20 Å2
2---3.895 Å20 Å2
3---12.634 Å2
Refinement stepCycle: LAST / Resolution: 2.85→62.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 65 37 6337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136472
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175492
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.658818
X-RAY DIFFRACTIONr_angle_other_deg1.1531.57512812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3835769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17423.92375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.059151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4761526
X-RAY DIFFRACTIONr_chiral_restr0.0490.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021401
X-RAY DIFFRACTIONr_nbd_refined0.1950.21209
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.25176
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23105
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.22667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2141
X-RAY DIFFRACTIONr_metal_ion_refined0.1810.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.25
X-RAY DIFFRACTIONr_nbd_other0.2270.222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2820.21
X-RAY DIFFRACTIONr_mcbond_it1.8957.4133079
X-RAY DIFFRACTIONr_mcbond_other1.8937.4123078
X-RAY DIFFRACTIONr_mcangle_it3.19411.1213847
X-RAY DIFFRACTIONr_mcangle_other3.19411.1223848
X-RAY DIFFRACTIONr_scbond_it1.6037.5273393
X-RAY DIFFRACTIONr_scbond_other1.6047.5253391
X-RAY DIFFRACTIONr_scangle_it2.82711.2484971
X-RAY DIFFRACTIONr_scangle_other2.82711.2484971
X-RAY DIFFRACTIONr_lrange_it4.83383.6827091
X-RAY DIFFRACTIONr_lrange_other4.83383.6967092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9240.3792160.4053769X-RAY DIFFRACTION100
2.924-3.0040.4351810.3933592X-RAY DIFFRACTION99.947
3.004-3.0910.3151780.3663569X-RAY DIFFRACTION99.9733
3.091-3.1860.3561620.3353456X-RAY DIFFRACTION99.862
3.186-3.2910.3141750.3183327X-RAY DIFFRACTION100
3.291-3.4060.2821710.2913223X-RAY DIFFRACTION99.9705
3.406-3.5350.2711610.2713096X-RAY DIFFRACTION100
3.535-3.6790.2681610.2513016X-RAY DIFFRACTION99.9371
3.679-3.8430.2481520.2282861X-RAY DIFFRACTION100
3.843-4.030.2571620.2132724X-RAY DIFFRACTION99.9307
4.03-4.2480.1951290.1852636X-RAY DIFFRACTION100
4.248-4.5060.1891230.1552531X-RAY DIFFRACTION100
4.506-4.8170.1461220.1262312X-RAY DIFFRACTION100
4.817-5.2030.1421390.1142146X-RAY DIFFRACTION100
5.203-5.6990.1651390.1341989X-RAY DIFFRACTION100
5.699-6.3710.181050.1481819X-RAY DIFFRACTION100
6.371-7.3560.206620.1511635X-RAY DIFFRACTION100
7.356-9.0070.151690.1351362X-RAY DIFFRACTION100
9.007-12.7270.13620.121069X-RAY DIFFRACTION100
12.727-160.32320.302624X-RAY DIFFRACTION98.9442

+
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