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- PDB-2zgg: Asn-hydroxylation stabilises the ankyrin repeat domain fold -

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Basic information

Entry
Database: PDB / ID: 2zgg
TitleAsn-hydroxylation stabilises the ankyrin repeat domain fold
Components3 repeat synthetic ankyrin
KeywordsDE NOVO PROTEIN / ankyrin repeat / unhydroxylated
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / : / :
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMcDonough, M.A. / Schofield, C.J.
Citation
Journal: Mol Biosyst / Year: 2009
Title: Asparagine beta-hydroxylation stabilizes the ankyrin repeat domain fold
Authors: Kelly, L. / McDonough, M.A. / Coleman, M.L. / Ratcliffe, P.J. / Schofield, C.J.
#1: Journal: J.Biol.Chem. / Year: 2007
Title: Asparaginyl hydroxylation of the Notch ankyrin repeat domain by factor inhibiting hypoxia-inducible factor
Authors: Coleman, M.L. / McDonough, M.A. / Hewitson, K.S. / Coles, C. / Mecinovic, J. / Edelmann, M. / Cook, K.M. / Cockman, M.E. / Lancaster, D.E. / Kessler, B.M. / Oldham, N.J. / Ratcliffe, P.J. / Schofield, C.J.
#2: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Posttranslational hydroxylation of ankyrin repeats in IkappaB proteins by the hypoxia-inducible factor (HIF) asparaginyl hydroxylase, factor inhibiting HIF (FIH)
Authors: Cockman, M.E. / Lancaster, D.E. / Stolze, I.P. / Hewitson, K.S. / McDonough, M.A. / Coleman, M.L. / Coles, C.H. / Yu, X. / Hay, R.T. / Ley, S.C. / Pugh, C.W. / Oldham, N.J. / Masson, N. / ...Authors: Cockman, M.E. / Lancaster, D.E. / Stolze, I.P. / Hewitson, K.S. / McDonough, M.A. / Coleman, M.L. / Coles, C.H. / Yu, X. / Hay, R.T. / Ley, S.C. / Pugh, C.W. / Oldham, N.J. / Masson, N. / Schofield, C.J. / Ratcliffe, P.J.
History
DepositionJan 21, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: 3 repeat synthetic ankyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9654
Polymers9,7351
Non-polymers2303
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 3 repeat synthetic ankyrin
hetero molecules

A: 3 repeat synthetic ankyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9308
Polymers19,4702
Non-polymers4616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area760 Å2
ΔGint-37 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.959, 48.959, 79.042
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-403-

CO

21A-1046-

HOH

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Components

#1: Protein 3 repeat synthetic ankyrin


Mass: 9734.885 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetically designed construct
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: 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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5mM MgCl2, 100mM HEPES, 5mM Co(II)Cl2, 5mM CdCl2, pH 7.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 29, 2005
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 7.5 % / Av σ(I) over netI: 9.2 / Number: 58446 / Rmerge(I) obs: 0.083 / Χ2: 1.01 / D res high: 2 Å / D res low: 50 Å / Num. obs: 7815 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315099.410.0421.0527
3.424.3110010.0431.0117.5
2.993.4210010.0651.0187.7
2.712.9910010.11.0137.7
2.522.7110010.1350.9767.8
2.372.5210010.1880.9647.8
2.252.3710010.2351.0067.7
2.152.2510010.2691.0077.6
2.072.1510010.3461.0297.3
22.0799.710.4441.0536.8
ReflectionResolution: 2→50 Å / Num. all: 7815 / Num. obs: 7815 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4.05 / Num. unique all: 761 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å28.91 Å
Translation2.5 Å28.91 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N0Q

1n0q


Resolution: 2→28.91 Å / Rfactor Rfree error: 0.009 / FOM work R set: 0.868 / Data cutoff high absF: 211914.016 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 697 9.3 %RANDOM
Rwork0.212 ---
all-7464 --
obs-7464 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 217.692 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å2-3.52 Å20 Å2
2---2.39 Å20 Å2
3---4.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms645 0 3 125 773
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it2.081.5
X-RAY DIFFRACTIONc_mcangle_it2.982
X-RAY DIFFRACTIONc_scbond_it3.082
X-RAY DIFFRACTIONc_scangle_it4.342.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.211 80 7 %
Rwork0.211 1067 -
all-1147 -
obs--90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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