[English] 日本語
Yorodumi
- PDB-1bv4: APO-MANNOSE-BINDING PROTEIN-C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bv4
TitleAPO-MANNOSE-BINDING PROTEIN-C
ComponentsPROTEIN (MANNOSE-BINDING PROTEIN-C)
KeywordsSUGAR BINDING PROTEIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN / COLLECTIN
Function / homology
Function and homology information


Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells ...Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / serine-type endopeptidase complex / phosphatidylinositol-4-phosphate binding / D-mannose binding / antiviral innate immune response / positive regulation of phagocytosis / multivesicular body / complement activation, classical pathway / calcium-dependent protein binding / : / protease binding / defense response to Gram-positive bacterium / innate immune response / signaling receptor binding / calcium ion binding / protein-containing complex / proteolysis / extracellular space / identical protein binding
Similarity search - Function
Collectin, C-type lectin-like domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like ...Collectin, C-type lectin-like domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Mannose-binding protein C
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNg, K.K.-S. / Weis, W.I.
CitationJournal: Biochemistry / Year: 1998
Title: Ca2+-dependent structural changes in C-type mannose-binding proteins.
Authors: Ng, K.K. / Park-Snyder, S. / Weis, W.I.
History
DepositionSep 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (MANNOSE-BINDING PROTEIN-C)
B: PROTEIN (MANNOSE-BINDING PROTEIN-C)
C: PROTEIN (MANNOSE-BINDING PROTEIN-C)
D: PROTEIN (MANNOSE-BINDING PROTEIN-C)


Theoretical massNumber of molelcules
Total (without water)52,6464
Polymers52,6464
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.390, 132.620, 46.810
Angle α, β, γ (deg.)90.00, 94.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.3982, -0.7381, 0.5446), (-0.7206, -0.6191, -0.3121), (0.5675, -0.2682, -0.7784)19.405, 9.061, -37.047
2given(0.9653, 0.2159, 0.1468), (0.2196, -0.9755, -0.0091), (0.1413, 0.041, -0.9891)0.56, 22.051, -26
3given(0.3635, -0.8525, 0.3757), (0.7764, 0.5001, 0.3836), (-0.5149, 0.1523, 0.8436)15.07, 18.324, 13.243

-
Components

#1: Protein
PROTEIN (MANNOSE-BINDING PROTEIN-C)


Mass: 13161.604 Da / Num. of mol.: 4 / Fragment: SUBTILISIN FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PINOMPAII / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JA221 / References: UniProt: P08661
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.18 Å3/Da / Density % sol: 36 %
Crystal growpH: 6.2
Details: 12% PEG 8000, 100 MM NAMES, PH 6.1, 200 MM LICL, 2 MM EDTA 0.02%, NAN3, pH 6.2
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
28-12 %(w/v)PEG80001reservoir
3100 mMTris-Cl1reservoirpH8.0
410 mM1reservoirNaCl
50.02 %1reservoirNaN3
60.375 mM1reservoirDyCl3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 33667 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.2 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.26

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS0.3Crefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RDO

1rdo


Resolution: 1.85→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3287 10 %RANDOM
Rwork0.212 ---
obs0.212 33070 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20.38 Å2
2---3.65 Å20 Å2
3---2.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-50 Å
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 0 234 3471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.41.5
X-RAY DIFFRACTIONc_mcangle_it3.392
X-RAY DIFFRACTIONc_scbond_it3.732
X-RAY DIFFRACTIONc_scangle_it5.182.5
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.304 290 10 %
Rwork0.237 2895 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 10 % / Rfactor Rwork: 0.237 / Rfactor obs: 0.237

+
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