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- PDB-2utg: STRUCTURE AND REFINEMENT OF THE OXIDIZED P21 FORM OF UTEROGLOBIN ... -

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Basic information

Entry
Database: PDB / ID: 2utg
TitleSTRUCTURE AND REFINEMENT OF THE OXIDIZED P21 FORM OF UTEROGLOBIN AT 1.64 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 / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Uteroglobin / Uteroglobin / Secretoglobin superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 1.64 Å
AuthorsBally, R. / Delettre, J.
CitationJournal: J.Mol.Biol. / Year: 1989
Title: Structure and refinement of the oxidized P21 form of uteroglobin at 1.64 A resolution.
Authors: Bally, R. / Delettre, J.
History
DepositionMay 17, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UTEROGLOBIN
B: UTEROGLOBIN


Theoretical massNumber of molelcules
Total (without water)15,8212
Polymers15,8212
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-40 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.560, 46.060, 37.430
Angle α, β, γ (deg.)90.00, 120.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UTEROGLOBIN


Mass: 7910.272 Da / Num. of mol.: 2
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.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal grow
*PLUS
Temperature: 38 ℃ / Method: vapor diffusion / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
250 mM1dropNaCl
3ammonium sulfate1reservoir

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Data collection

Reflection
*PLUS

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.19 / Highest resolution: 1.64 Å
Refinement stepCycle: LAST / Highest resolution: 1.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1096 0 0 165 1261
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0580.05
X-RAY DIFFRACTIONp_angle_d0.1080.1
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.1090.1
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6271
X-RAY DIFFRACTIONp_mcangle_it1.0411.5
X-RAY DIFFRACTIONp_scbond_it0.6931
X-RAY DIFFRACTIONp_scangle_it1.1291.5
X-RAY DIFFRACTIONp_plane_restr0.0290.05
X-RAY DIFFRACTIONp_chiral_restr0.210.25
X-RAY DIFFRACTIONp_singtor_nbd0.20.5
X-RAY DIFFRACTIONp_multtor_nbd0.1580.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1990.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.810
X-RAY DIFFRACTIONp_staggered_tor2115
X-RAY DIFFRACTIONp_orthonormal_tor22.215
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.64 Å / Num. reflection obs: 8866 / σ(F): 2 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 10.4 Å2

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