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- PDB-1sdi: 1.65 A structure of Escherichia coli ycfC gene product -

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Basic information

Entry
Database: PDB / ID: 1sdi
Title1.65 A structure of Escherichia coli ycfC gene product
ComponentsHypothetical protein ycfC
Keywordsstructural genomics / unknown function / paracytosis / peripheral membrane protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


response to heat / plasma membrane / cytoplasm
Similarity search - Function
YcfC-like / HflD-like / High frequency lysogenization protein HflD / HflD-like superfamily / Protein of unknown function (DUF489) / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / High frequency lysogenization protein HflD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 1.65 Å
AuthorsBorek, D. / Otwinowski, Z. / Chen, Y. / Skarina, T. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structural analysis of Escherichia coli ycfC gene product
Authors: Borek, D. / Otwinowski, Z. / Chen, Y. / Skarina, T. / Savchenko, A. / Edwards, A.
History
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ycfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1364
Polymers22,8971
Non-polymers2383
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.527, 62.649, 68.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein ycfC / ORF-23


Mass: 22897.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YCFC, B1132 / Production host: Escherichia coli (E. coli) / References: UniProt: P25746
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 14, 2003
RadiationMonochromator: Rosenbaum-Rock monochromator #1 high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator #2 double crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 22718 / Num. obs: 21058 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 11.96 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 17.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1347 / % possible all: 60.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: isomorphous replacement / Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.736 / SU ML: 0.058 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18386 221 1.1 %RANDOM
Rwork0.15014 ---
all0.1503 22698 --
obs0.1505 20765 92.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 0 201 1858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0211694
X-RAY DIFFRACTIONr_bond_other_d0.0020.021623
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.9672298
X-RAY DIFFRACTIONr_angle_other_deg0.95733756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945214
X-RAY DIFFRACTIONr_chiral_restr0.110.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021869
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02321
X-RAY DIFFRACTIONr_nbd_refined0.2390.2373
X-RAY DIFFRACTIONr_nbd_other0.240.21762
X-RAY DIFFRACTIONr_nbtor_other0.0880.2984
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0850.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.228
X-RAY DIFFRACTIONr_mcbond_it1.57921073
X-RAY DIFFRACTIONr_mcangle_it2.57331721
X-RAY DIFFRACTIONr_scbond_it2.3122621
X-RAY DIFFRACTIONr_scangle_it3.6353576
LS refinement shellResolution: 1.65→1.694 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 1
Rwork0.174 943

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