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- PDB-1yln: The Crystal Structure of the Protein of Unknown Function VCA0042 ... -

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Basic information

Entry
Database: PDB / ID: 1yln
TitleThe Crystal Structure of the Protein of Unknown Function VCA0042 from Vibrio cholerae O1
Componentshypothetical protein vca0042
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Vibrio cholerae O1 / beta barrels / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


bacterial-type flagellum basal body / cyclic-di-GMP binding
Similarity search - Function
Flagellar protein YcgR / Type III secretion system flagellar brake protein YcgR, PilZN domain / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Thrombin, subunit H / Roll ...Flagellar protein YcgR / Type III secretion system flagellar brake protein YcgR, PilZN domain / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Thrombin, subunit H / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Cyclic di-GMP binding protein VCA0042
Similarity search - Component
Biological speciesVibrio cholerae O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the hypothetical protein vca0042 from Vibrio cholerae O1
Authors: Zhang, R. / Zhou, M. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein vca0042


Theoretical massNumber of molelcules
Total (without water)28,4991
Polymers28,4991
Non-polymers00
Water2,432135
1
A: hypothetical protein vca0042

A: hypothetical protein vca0042


Theoretical massNumber of molelcules
Total (without water)56,9972
Polymers56,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)56.429, 56.429, 171.128
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThis trotein exists as dimer. The second part of the biological assembly is generated by : y, x,-z

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Components

#1: Protein hypothetical protein vca0042


Mass: 28498.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Species: Vibrio cholerae / Strain: N16961 / Gene: GI:9657424 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 9657424, UniProt: Q9KNC3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.714 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M K/Na tartrate, 0.1M Tris, 0.2M Li2SO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 25, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 30326 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 14.83
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.04 / Num. unique all: 1652 / % possible all: 95.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→32.19 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 220916.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used "HLML" target in CNS refinement in which the friedel's pair was treated as two seperated reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1366 4.9 %RANDOM
Rwork0.21 ---
obs0.21 27829 89.9 %-
all-30956 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.1882 Å2 / ksol: 0.351434 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å23.58 Å20 Å2
2--3.28 Å20 Å2
3----6.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 0 135 1928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 208 5.6 %
Rwork0.334 3532 -
obs--72 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP1.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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