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- PDB-1vmo: CRYSTAL STRUCTURE OF VITELLINE MEMBRANE OUTER LAYER PROTEIN I (VM... -

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Basic information

Entry
Database: PDB / ID: 1vmo
TitleCRYSTAL STRUCTURE OF VITELLINE MEMBRANE OUTER LAYER PROTEIN I (VMO-I): A FOLDING MOTIF WITH HOMOLOGOUS GREEK KEY STRUCTURES RELATED BY AN INTERNAL THREE-FOLD SYMMETRY
ComponentsVITELLINE MEMBRANE OUTER LAYER PROTEIN I
KeywordsMEMBRANE PROTEIN
Function / homologyVitelline membrane outer layer protein I (VOMI) / Vitelline membrane outer layer protein I (VOMI) / Vitelline membrane outer layer protein I (VOMI) superfamily / Vitelline membrane outer layer protein I (VOMI) / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / extracellular space / Mainly Beta / Vitelline membrane outer layer protein 1
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsShimizu, T. / Vassylyev, D.G. / Kido, S. / Doi, Y. / Morikawa, K.
Citation
Journal: EMBO J. / Year: 1994
Title: Crystal structure of vitelline membrane outer layer protein I (VMO-I): a folding motif with homologous Greek key structures related by an internal three-fold symmetry.
Authors: Shimizu, T. / Vassylyev, D.G. / Kido, S. / Doi, Y. / Morikawa, K.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary Crystallographic Data of Vitelline Membrane Outer Layer Protein 1 Vmo1
Authors: Shimizu, T. / Morikawa, K. / Kido, S. / Doi, Y.
History
DepositionJan 6, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VITELLINE MEMBRANE OUTER LAYER PROTEIN I
B: VITELLINE MEMBRANE OUTER LAYER PROTEIN I


Theoretical massNumber of molelcules
Total (without water)36,0012
Polymers36,0012
Non-polymers00
Water2,594144
1
A: VITELLINE MEMBRANE OUTER LAYER PROTEIN I


Theoretical massNumber of molelcules
Total (without water)18,0001
Polymers18,0001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VITELLINE MEMBRANE OUTER LAYER PROTEIN I


Theoretical massNumber of molelcules
Total (without water)18,0001
Polymers18,0001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.420, 110.510, 44.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9941, 0.10496, 0.02729), (-0.10708, 0.98984, 0.09353), (-0.0172, -0.0959, 0.99524)
Vector: 32.223, 2.486, 12.491)

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Components

#1: Protein VITELLINE MEMBRANE OUTER LAYER PROTEIN I


Mass: 18000.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P41366
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE HAS NOT BEEN REPORTED. A PAPER DESCRIBING THE SEQUENCE IS IN PREPARATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125-30 mg/mlprotein1drop
250 mM1dropKCl
33 %(w/v)PEG40001drop
446.7 mMacetate1drop
55 %(w/v)PEG40001reservoir
6100 mM1reservoirKCl

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 13489 / % possible obs: 83.4 % / Rmerge(I) obs: 0.0459

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.188 -
obs0.188 12661
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 0 144 2674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.83
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.188 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.83
X-RAY DIFFRACTIONx_improper_angle_d0.012

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