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- PDB-1nnx: Structure of the hypothetical protein ygiW from E. coli. -

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Basic information

Entry
Database: PDB / ID: 1nnx
TitleStructure of the hypothetical protein ygiW from E. coli.
ComponentsProtein ygiW
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ygiW / hypothetical protein / OB-fold / Structure 2 Function Project / S2F
Function / homology
Function and homology information


single-species biofilm formation on inanimate substrate / cellular response to cadmium ion / cellular response to hydrogen peroxide / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
Bacterial OB-fold / Bacterial OB-fold / YgiW/YdeI / Bacterial OB-fold superfamily / : / Bacterial OB fold (BOF) protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protein YgiW / Protein YgiW
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsLehmann, C. / Galkin, A. / Pullalarevu, S. / Sarikaya, E. / Krajewski, W. / Lim, K. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: To be Published
Title: Structure of the hypothetical protein ygiW from E. coli.
Authors: Lehmann, C. / Galkin, A. / Pullalarevu, S. / Sarikaya, E. / Krajewski, W. / Lim, K. / Howard, A. / Herzberg, O.
History
DepositionJan 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Protein ygiW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0142
Polymers11,9181
Non-polymers961
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.802, 60.638, 54.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1023-

HOH

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Components

#1: Protein Protein ygiW


Mass: 11918.005 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YGIW / Plasmid: pYGIW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P52083, UniProt: P0ADU5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.89 Å3/Da / Density % sol: 35.68 %
Crystal growTemperature: 294 K / pH: 2.4
Details: 1.25 M (NH4)2SO4, 0.1 M Na acetate, pH 2.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 2.40

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2002 / Details: MIRROR
RadiationMonochromator: SI(111) DOUBLE CRYSTAL SYSTEM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→27.4 Å / Num. obs: 15321 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 0.93 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.73
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 0.77 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.07 / % possible all: 77.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
SHELXmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.45→9.94 Å / Rfactor Rfree error: 0.008 / Num. parameters: 8321 / Num. restraintsaints: 10416 / Data cutoff high absF: 973969.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1030 7 %RANDOM
Rwork0.196 ---
obs0.196 14682 89 %-
all-14208 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6835 Å2 / ksol: 0.304212 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.79 Å20 Å20 Å2
2--3.44 Å20 Å2
3---1.34 Å2
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 854.5
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-10 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.45→9.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 5 125 910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.51.5
X-RAY DIFFRACTIONc_mcangle_it3.692
X-RAY DIFFRACTIONc_scbond_it4.652
X-RAY DIFFRACTIONc_scangle_it6.512.5
LS refinement shellResolution: 1.45→1.5 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3 64 6.7 %
Rwork0.273 887 -
obs--59.3 %

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