[English] 日本語
Yorodumi
- PDB-6j6f: Ligand binding domain 1 and 2 of Talaromyces marneffei Mp1 protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j6f
TitleLigand binding domain 1 and 2 of Talaromyces marneffei Mp1 protein
ComponentsEnvelope glycoprotein
KeywordsLIPID BINDING PROTEIN / T.marenffei Mp1p
Function / homologyCell wall mannoprotein 1 / Hydrophobic surface binding protein A / extracellular region / NICKEL (II) ION / Envelope glycoprotein
Function and homology information
Biological speciesTalaromyces marneffei PM1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å
AuthorsLam, W.H. / Zhang, H. / Hao, Q.
CitationJournal: Infect. Immun. / Year: 2019
Title: Talaromyces marneffeiMp1 Protein, a Novel Virulence Factor, Carries Two Arachidonic Acid-Binding Domains To Suppress Inflammatory Responses in Hosts.
Authors: Lam, W.H. / Sze, K.H. / Ke, Y. / Tse, M.K. / Zhang, H. / Woo, P.C.Y. / Lau, S.K.P. / Lau, C.C.Y. / Xu, S. / Lai, P.M. / Zhou, T. / Antonyuk, S.V. / Kao, R.Y.T. / Yuen, K.Y. / Hao, Q.
History
DepositionJan 15, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 6, 2019ID: 5X3Q
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5574
Polymers66,4402
Non-polymers1172
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.393, 146.393, 148.611
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A16 - 323
2111B16 - 323

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.281932, 0.959433, 0.00137), (0.959434, 0.28193, 0.001562), (0.001113, 0.001755, -0.999998)-93.891281, 70.221222, 16.320459

-
Components

#1: Protein Envelope glycoprotein / Mp1p


Mass: 33219.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces marneffei PM1 (fungus) / Gene: MP1 / Plasmid: His-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A093VKV7
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.01 Å3/Da / Density % sol: 79.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.1M Tris-HCl, 10mM NiCl2, 1.1M Li2SO4, 5% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 12272 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.153 / Χ2: 0.982 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsΧ2Diffraction-ID% possible allRmerge(I) obs
4.2-4.356.311890.9911100
4.35-4.526.312051.10611000.902
4.52-4.736.312170.94911000.694
4.73-4.986.312000.98311000.528
4.98-5.296.312050.98211000.462
5.29-5.76.312100.98911000.495
5.7-6.276.112310.99511000.41
6.27-7.18612310.92199.70.167
7.18-9.03612610.949199.80.079
9.03-505.713230.953197.30.102

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.74 Å41.03 Å
Translation6.74 Å41.03 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FB7

5fb7


Resolution: 4.2→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.896 / SU B: 88.122 / SU ML: 1.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.784
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3496 547 4.5 %RANDOM
Rwork0.2943 ---
obs0.2967 11685 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 364.26 Å2 / Biso mean: 93.425 Å2 / Biso min: 44.81 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å2-0 Å2-0 Å2
2--3.88 Å2-0 Å2
3----7.76 Å2
Refinement stepCycle: final / Resolution: 4.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 2 0 3217
Biso mean--89.74 --
Num. residues----622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193254
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9444533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14723.15819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6341529
X-RAY DIFFRACTIONr_chiral_restr0.0880.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212700
Refine LS restraints NCSNumber: 308 / Type: TIGHT THERMAL / Rms dev position: 14.93 Å / Weight position: 0.5
LS refinement shellResolution: 4.202→4.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 61 -
Rwork0.435 824 -
all-885 -
obs--99.66 %

+
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