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- PDB-2b8i: Crystal Structure and Functional Studies Reveal that PAS Factor f... -

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Basic information

Entry
Database: PDB / ID: 2b8i
TitleCrystal Structure and Functional Studies Reveal that PAS Factor from Vibrio vulnificus is a Novel Member of the Saposin-Fold Family
ComponentsPAS factor
KeywordsLIPID BINDING PROTEIN / Four helix bundle
Function / homologyPas factor, saposin domain / Pas factor saposin domain / Pas factor saposin fold / Monooxygenase / Up-down Bundle / Mainly Alpha / : / Secretion factor PAS
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLee, J.H. / Yang, S.T. / Rho, S.H. / Im, Y.J. / Kim, S.Y. / Kim, Y.R. / Kim, M.K. / Kang, G.B. / Kim, J.I. / Rhee, J.H. / Eom, S.H.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure and functional studies reveal that PAS factor from Vibrio vulnificus is a novel member of the saposin-fold family
Authors: Lee, J.H. / Yang, S.T. / Rho, S.H. / Im, Y.J. / Kim, S.Y. / Kim, Y.R. / Kim, M.K. / Kang, G.B. / Kim, J.I. / Rhee, J.H. / Eom, S.H.
History
DepositionOct 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PAS factor


Theoretical massNumber of molelcules
Total (without water)8,5721
Polymers8,5721
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.157, 75.192, 80.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein PAS factor


Mass: 8571.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 37679996, UniProt: Q56GA4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 22% (w/v) PEG 4000, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 7767 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 92

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.232 162 RANDOM
Rwork0.199 --
all0.201 --
obs0.2 7141 -
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms604 0 0 29 633
Refine LS restraintsType: r_bond_d / Dev ideal: 0.009

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