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- PDB-3ffv: Crystal Structure Analysis of Syd -

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Basic information

Entry
Database: PDB / ID: 3ffv
TitleCrystal Structure Analysis of Syd
ComponentsProtein syd
KeywordsPROTEIN BINDING / Membrane / Translocon / SecYEG / Syd / Nanodisc / Cell inner membrane / Cell membrane
Function / homology
Function and homology information


regulation of protein-containing complex assembly / cytoplasmic side of plasma membrane / cytoplasm
Similarity search - Function
Syd protein / Syd / Syd superfamily / Syd protein (SUKH-2) / SMI1/KNR4-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMaurus, R. / Brayer, G.D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure, Binding, and Activity of Syd, a SecY-interacting Protein
Authors: Dalal, K. / Nguyen, N. / Alami, M. / Tan, J. / Moraes, T.F. / Lee, W.C. / Maurus, R. / Sligar, S.S. / Brayer, G.D. / Duong, F.
History
DepositionDec 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 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: Protein syd
B: Protein syd


Theoretical massNumber of molelcules
Total (without water)41,4592
Polymers41,4592
Non-polymers00
Water9,188510
1
A: Protein syd


Theoretical massNumber of molelcules
Total (without water)20,7291
Polymers20,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein syd


Theoretical massNumber of molelcules
Total (without water)20,7291
Polymers20,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)167.600, 167.600, 41.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Protein syd


Mass: 20729.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A8U0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 298 K / pH: 7
Details: 0.8-1.0 M sodium citrate, 0.2 M sodium chloride, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9788
DetectorType: MARMOSAIC 325 MM CCD MARMOSAIC 325 MM CCD / Detector: CCD / Date: Jun 9, 2007
Details: FLAT MIRROR (VERTICAL FOCUSING); SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HO RIZONTAL FOCUSING); FLAT MIRROR (VERTICAL FOCUSING); SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SIDE SCATTERING BENT CUBE- ROOT I-BEAM SINGLE CRYSTAL; ASYMMETRIC CUT 4.965 DEGS; SIDE SCATTERING BENT CUBE-ROOT I-BEAM SINGLE CRYSTAL; ASYMMETRIC CUT 4.965 DEGSSINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29401 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.068
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 8.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→41.9 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1442 -RANDOM
Rwork0.182 ---
obs0.182 29401 99.8 %-
all-29447 --
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 0 510 3430

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