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- PDB-3hnw: Crystal Structure of a Basic Coiled-Coil Protein of Unknown Funct... -

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Basic information

Entry
Database: PDB / ID: 3hnw
TitleCrystal Structure of a Basic Coiled-Coil Protein of Unknown Function from Eubacterium eligens ATCC 27750
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / coiled-coil / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #790 / : / Cell division protein ZapA-like / Cell division protein ZapA-like superfamily / Cell division protein ZapA / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
IODIDE ION / Cell division protein ZapA
Similarity search - Component
Biological speciesEubacterium eligens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.196 Å
AuthorsKim, Y. / Hendricks, R. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of a Basic Coiled-Coil Protein of Unknown Function from Eubacterium eligens ATCC 27750
Authors: Kim, Y. / Cuff, M. / Hendricks, R. / Keigher, L. / Joachimiak, A.
History
DepositionJun 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 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 / struct_site
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.db_align_beg / _struct_ref_seq.db_align_end / _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: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,32011
Polymers32,3172
Non-polymers1,0039
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-66 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.182, 53.837, 40.917
Angle α, β, γ (deg.)90.00, 99.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-185-

HOH

21B-175-

HOH

31B-190-

HOH

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Components

#1: Protein uncharacterized protein


Mass: 16158.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium eligens (bacteria) / Strain: ATCC 27750 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: D0VWZ2*PLUS
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.88 Å3/Da / Density % sol: 68.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.3M Na Iodide, 10% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 3, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.196→27.85 Å / Num. all: 25331 / Num. obs: 25331 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 43.67 Å2 / Rsym value: 0.088 / Net I/σ(I): 13
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1251 / Rsym value: 0.392 / % possible all: 97.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.4_58)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.196→27.849 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TWIN_LSQ_F / Details: twin_law=-h-2*l, -k,l
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1300 5.13 %random
Rwork0.213 ---
all0.215 25331 --
obs0.215 25321 99.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.945 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.9344 Å20 Å2-1.0738 Å2
2--6.3303 Å2-0 Å2
3---9.604 Å2
Refinement stepCycle: LAST / Resolution: 2.196→27.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 29 179 2286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_deg1.229
X-RAY DIFFRACTIONf_dihedral_angle_d23.537
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1992-2.28710.31351150.2862648276394
2.2871-2.3910.28751420.28672664280695
2.391-2.51670.31461340.29422649278395
2.5167-2.6740.31061450.2732643278895
2.674-2.87970.29181350.27842688282395
2.8797-3.16820.32211530.25162661281494
3.1682-3.62360.23031480.2042676282495
3.6236-4.55410.19021480.14952696284494
4.5541-18.47070.22611670.19092659282692

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