[English] 日本語
Yorodumi
- PDB-1utg: REFINEMENT OF THE C2221 CRYSTAL FORM OF OXIDIZED UTEROGLOBIN AT 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1utg
TitleREFINEMENT OF THE C2221 CRYSTAL FORM OF OXIDIZED UTEROGLOBIN AT 1.34 ANGSTROMS RESOLUTION
ComponentsUTEROGLOBIN
KeywordsSTEROID BINDING
Function / homology
Function and homology information


phospholipase A2 inhibitor activity / steroid binding / signal transduction / extracellular space / cytoplasm
Similarity search - Function
Secretoglobin / Uteroglobin / Secretoglobin family 1C-like / Uteroglobin / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Uteroglobin / Secretoglobin superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 1.34 Å
AuthorsMorize, I. / Surcouf, E. / Vaney, M.C. / Buehner, M. / Mornon, J.P.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Refinement of the C222(1) crystal form of oxidized uteroglobin at 1.34 A resolution.
Authors: Morize, I. / Surcouf, E. / Vaney, M.C. / Epelboin, Y. / Buehner, M. / Fridlansky, F. / Milgrom, E. / Mornon, J.P.
#1: Journal: FEBS Lett. / Year: 1988
Title: Evidence for the Identity of Anti-Proteinase Pulmonary Protein Ccsp and Uteroglobin
Authors: Lopez Deharo, M.S. / Alvarez, L. / Nieto, A.
#2: Journal: Biochem.J. / Year: 1987
Title: Purification, Characterization and Proteinase-Inhibitory Activity of a Clara-Cell Secretory Protein from the Pulmonary Extracellular Lining of Rabbits
Authors: Gupta, R.P. / Patton, S.E. / Jetten, A.M. / Hook, G.E.R.
#3: Journal: Endocr.Rev. / Year: 1987
Title: Uteroglobin. Structure, Molecular Biology, and New Perspectives on its Function as a Phospholipasea2 Inhibitor
Authors: Miele, L. / Cordella-Miele, E. / Mukherjee, A.B.
#4: Journal: J.Mol.Biol. / Year: 1982
Title: Use of Molecular Replacement in the Structure Determination of the P21212 and the P21 (Pseudo P21212) Crystal Forms of Oxidized Uteroglobin
Authors: Buehner, M. / Lifchitz, A. / Bally, R. / Mornon, J.P.
#5: Journal: J.Mol.Biol. / Year: 1980
Title: X-Ray Crystallographic Analysis of a Progesterone-Binding Protein. The C 2 2 21 Crystal Form of Oxidized Uteroglobin at 2.2 Angstroms Resolution
Authors: Mornon, J.P. / Fridlansky, F. / Bally, R. / Milgrom, E.
#6: Journal: J.Mol.Biol. / Year: 1979
Title: Characterization of Two New Crystal Forms of Uteroglobin
Authors: Mornon, J.P. / Bally, R. / Fridlansky, F. / Milgrom, E.
#7: Journal: J.Mol.Biol. / Year: 1978
Title: X-Ray Analysis of a Progesterone-Binding Protein (Uteroglobin). Preliminary Results
Authors: Mornon, J.P. / Surcouf, E. / Bally, R. / Fridlansky, F. / Milgrom, E.
History
DepositionApr 3, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UTEROGLOBIN


Theoretical massNumber of molelcules
Total (without water)7,9101
Polymers7,9101
Non-polymers00
Water1,49583
1
A: UTEROGLOBIN

A: UTEROGLOBIN


Theoretical massNumber of molelcules
Total (without water)15,8212
Polymers15,8212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area2930 Å2
ΔGint-39 kcal/mol
Surface area7470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.860, 52.220, 47.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: SEE REMARK 5.
Components on special symmetry positions
IDModelComponents
11A-147-

HOH

-
Components

#1: Protein UTEROGLOBIN


Mass: 7910.272 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / References: UniProt: P02779
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURE CONSISTS OF FOUR ALPHA-HELICES AND ONE BETA-TURN PER MONOMER. A CAVITY ...THE SECONDARY STRUCTURE CONSISTS OF FOUR ALPHA-HELICES AND ONE BETA-TURN PER MONOMER. A CAVITY EXISTS IN THE DIMER, BETWEEN THE TWO MONOMERS. ITS LENGTH IS 15.6 ANGSTROMS AND ITS WIDTH IS 9. ANGSTROMS. 14 WATER MOLECULES POSITIONS COULD BE RECOGNISED AS DISORDERED INSIDE THE CAVITY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal grow
*PLUS
Method: vapor diffusion / Details: took from Mornon et al., from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
250 mMTris-HCl1drop
350 mM1dropNaCl
4ammonium sulfate1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 1.34 Å / Lowest resolution: 22 Å / Num. obs: 7509 / Rmerge(I) obs: 0.089

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.23 / Highest resolution: 1.34 Å
Refinement stepCycle: LAST / Highest resolution: 1.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms548 0 0 83 631
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.014
X-RAY DIFFRACTIONp_angle_d0.0410.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0080.016
X-RAY DIFFRACTIONp_chiral_restr0.2040.13
X-RAY DIFFRACTIONp_singtor_nbd0.2790.35
X-RAY DIFFRACTIONp_multtor_nbd0.130.35
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1770.35
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.12.5
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / Num. reflection obs: 14227 / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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