[English] 日本語
Yorodumi
- PDB-4pf0: Structure of the E502A variant of sacteLam55A from Streptomyces s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pf0
TitleStructure of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with laminarihexaose
ComponentsPutative secreted protein
KeywordsHYDROLASE / exo-beta-1 / 3-glucanase / beta-1 / GH55 / laminaritetraose / secreted / biomass degradation
Function / homologyglucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / glucan catabolic process / Pectin lyase fold / extracellular region / Exo-beta-1,3-glucanase
Function and homology information
Biological speciesStreptomyces sp. SirexAA-E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsBianchetti, C.M. / Takasuka, T.E. / Yik, E.J. / Bergeman, L.F. / Fox, B.G.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Active site and laminarin binding in glycoside hydrolase family 55.
Authors: Bianchetti, C.M. / Takasuka, T.E. / Deutsch, S. / Udell, H.S. / Yik, E.J. / Bergeman, L.F. / Fox, B.G.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Apr 1, 2015Group: Atomic model / Derived calculations
Revision 1.3May 20, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
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 / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative secreted protein
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9098
Polymers120,1452
Non-polymers3,7636
Water24,4281356
1
A: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9544
Polymers60,0731
Non-polymers1,8823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9544
Polymers60,0731
Non-polymers1,8823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.098, 100.960, 104.176
Angle α, β, γ (deg.)90.00, 91.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Putative secreted protein


Mass: 60072.637 Da / Num. of mol.: 2 / Fragment: UNP residues 46-605
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SirexAA-E (bacteria) / Gene: SACTE_4363 / Plasmid: PVP67K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G2NFJ9
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1356 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, and 0.010 M MOPS pH 7) mixed in a 1:1 ratio with the Well Solution (20% PEG 3350, 200mM NaC2H302, and 100mM BTP pH 6.0). Cryoprotected with ...Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, and 0.010 M MOPS pH 7) mixed in a 1:1 ratio with the Well Solution (20% PEG 3350, 200mM NaC2H302, and 100mM BTP pH 6.0). Cryoprotected with 20% PEG 3350, 200mM NaC2H302, 25mM laminaritetraose, 100mM BTP pH 6.0 and 15% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Number: 538788 / Rmerge(I) obs: 0.096 / Χ2: 0.88 / D res high: 1.64 Å / D res low: 50 Å / Num. obs: 136258 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.455010.0370.4384.1
3.534.4510.0470.5944.2
3.093.5310.0690.9354.2
2.83.0910.0790.954.2
2.62.810.090.9834.2
2.452.610.0980.9964.2
2.332.4510.1051.0184.1
2.232.3310.1191.0654.1
2.142.2310.1251.0374.1
2.072.1410.1341.0324.1
22.0710.1461.0044
1.94210.160.9464
1.891.9410.1820.9444
1.851.8910.2140.8744
1.811.8510.2430.8234
1.771.8110.2740.8063.9
1.731.7710.3330.7743.9
1.71.7310.3440.7493.5
1.671.710.3940.723.3
1.641.6710.4480.7113.1
ReflectionResolution: 1.64→50 Å / Num. obs: 136258 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 15.66 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.6
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.448 / % possible all: 96.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PEW

4pew


Resolution: 1.75→30.3 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 5635 5.03 %
Rwork0.151 --
obs0.152 112136 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→30.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8325 0 254 1356 9935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079032
X-RAY DIFFRACTIONf_angle_d1.13412365
X-RAY DIFFRACTIONf_dihedral_angle_d12.083269
X-RAY DIFFRACTIONf_chiral_restr0.0471389
X-RAY DIFFRACTIONf_plane_restr0.0061616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.2461850.19253425X-RAY DIFFRACTION97
1.7699-1.79070.21081920.18433505X-RAY DIFFRACTION99
1.7907-1.81250.2361800.17053505X-RAY DIFFRACTION99
1.8125-1.83550.19861760.1763536X-RAY DIFFRACTION99
1.8355-1.85960.1921940.17243543X-RAY DIFFRACTION100
1.8596-1.88510.23431820.17133480X-RAY DIFFRACTION99
1.8851-1.9120.22291920.16823576X-RAY DIFFRACTION100
1.912-1.94060.18841700.15513596X-RAY DIFFRACTION100
1.9406-1.97090.17361890.15933511X-RAY DIFFRACTION100
1.9709-2.00320.20291910.1543578X-RAY DIFFRACTION100
2.0032-2.03770.19551790.1453498X-RAY DIFFRACTION100
2.0377-2.07480.1711970.14963597X-RAY DIFFRACTION100
2.0748-2.11470.19521870.15393514X-RAY DIFFRACTION100
2.1147-2.15780.18571760.15233591X-RAY DIFFRACTION100
2.1578-2.20470.18511990.15223518X-RAY DIFFRACTION100
2.2047-2.2560.19191950.15093571X-RAY DIFFRACTION100
2.256-2.31240.20111820.16423518X-RAY DIFFRACTION100
2.3124-2.37490.21031900.15523583X-RAY DIFFRACTION100
2.3749-2.44470.21051920.15753539X-RAY DIFFRACTION100
2.4447-2.52360.20151860.15473563X-RAY DIFFRACTION100
2.5236-2.61380.20151920.16043558X-RAY DIFFRACTION100
2.6138-2.71830.19251830.1553578X-RAY DIFFRACTION100
2.7183-2.8420.20781940.16153569X-RAY DIFFRACTION100
2.842-2.99170.20531940.15393560X-RAY DIFFRACTION100
2.9917-3.17890.15671780.15323588X-RAY DIFFRACTION100
3.1789-3.42410.17311900.14813551X-RAY DIFFRACTION100
3.4241-3.76810.16671860.13763562X-RAY DIFFRACTION100
3.7681-4.3120.14532040.12713581X-RAY DIFFRACTION100
4.312-5.42760.12991830.11863609X-RAY DIFFRACTION99
5.4276-30.30220.16731970.15583598X-RAY DIFFRACTION99

+
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