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- PDB-3hra: Crystal Structure of EF0377 an Ankyrin Repeat Protein -

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Basic information

Entry
Database: PDB / ID: 3hra
TitleCrystal Structure of EF0377 an Ankyrin Repeat Protein
ComponentsAnkyrin repeat family protein
KeywordsSTRUCTURAL PROTEIN / Ankyrin Repeat
Function / homology
Function and homology information


Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Ankyrin repeat family protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.693 Å
AuthorsIsaacs, N.W. / Mitchell, T.J. / Riboldi-Tunnicliffe, A.
CitationJournal: To be Published
Title: Crystal Structure of EF0377 an Ankyrin Repeat
Authors: Isaacs, N.W. / Mitchell, T.J. / Bent, C.J. / Riboldi-Tunnicliffe, A.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Ankyrin repeat family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3952
Polymers22,3601
Non-polymers351
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.961, 66.902, 94.959
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 Ankyrin repeat family protein


Mass: 22359.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF0377 / Plasmid: pQE10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q838Q8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1.92 Å3/Da / Density % sol: 35.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4K, 100mM Tris, 200mM Sodium Acetate Trihydrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9755 Å
DetectorDetector: CCD / Date: Jun 2, 2002
RadiationMonochromator: liq. N2 cooled Si-111 double crystal or Si-111 channel cut monochromators (in series)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 1.69→31.551 Å / Num. all: 19959 / Num. obs: 16577 / % possible obs: 83.26 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 12.37 Å2 / Rsym value: 0.127 / Net I/σ(I): 3.9
Reflection shellResolution: 1.6928→1.7988 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NFI Chain E

1nfi


Resolution: 1.693→31.551 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.87 / SU ML: 0.18 / Isotropic thermal model: Overall / σ(F): 1.87 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.202 844 5.09 %Random
Rwork0.158 15733 --
obs0.161 16577 83.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.766 Å2 / ksol: 0.416 e/Å3
Displacement parametersBiso max: 50.76 Å2 / Biso mean: 14.289 Å2 / Biso min: 1.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.078 Å20 Å2-0 Å2
2---0.164 Å20 Å2
3----1.914 Å2
Refinement stepCycle: LAST / Resolution: 1.693→31.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 1 247 1802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081574
X-RAY DIFFRACTIONf_angle_d1.0262131
X-RAY DIFFRACTIONf_chiral_restr0.074239
X-RAY DIFFRACTIONf_plane_restr0.004287
X-RAY DIFFRACTIONf_dihedral_angle_d16.922579
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.693-1.7990.243730.1731279135242
1.799-1.9380.2081200.1582417253778
1.938-2.1330.2161540.1462710286488
2.133-2.4410.2031680.1462949311794
2.441-3.0750.2161550.163087324298
3.075-31.5560.1771740.1573291346599
Refinement TLS params.Method: refined / Origin x: -7.9555 Å / Origin y: 6.4953 Å / Origin z: -9.4444 Å
111213212223313233
T0.0032 Å20.0013 Å20.0054 Å2-0.011 Å2-0.0045 Å2--0.0067 Å2
L0.4215 °20.252 °2-0.3311 °2-0.5062 °2-0.4001 °2--0.3978 °2
S-0.0049 Å °-0.0401 Å °0.0369 Å °0.0247 Å °-0.006 Å °-0.006 Å °-0.0078 Å °0.0235 Å °0.0062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 201
2X-RAY DIFFRACTION1allA1 - 202
3X-RAY DIFFRACTION1allA1 - 247

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