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- PDB-4plr: Crystal Structures of Designed Armadillo Repeat Proteins: Implica... -

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Basic information

Entry
Database: PDB / ID: 4plr
TitleCrystal Structures of Designed Armadillo Repeat Proteins: Implications of Construct Design and Crystallization Conditions on Overall Structure.
ComponentsArm00008
KeywordsPEPTIDE BINDING PROTEIN / designed armadillo repeat proteins / protein engineering
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsReichen, C. / Madhurantakam, C. / Plueckthun, A. / Mittl, P.
CitationJournal: Protein Sci. / Year: 2014
Title: Crystal structures of designed armadillo repeat proteins: Implications of construct design and crystallization conditions on overall structure.
Authors: Reichen, C. / Madhurantakam, C. / Pluckthun, A. / Mittl, P.R.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Dec 20, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arm00008
B: Arm00008
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,13410
Polymers60,8142
Non-polymers3218
Water4,197233
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-60 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.054, 116.054, 86.932
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-303-

CA

21B-303-

CA

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Components

#1: Protein Arm00008


Mass: 30406.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: synthetic compound / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18 % PEG 8000, 0.2 M calcium acetate, 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→82.062 Å / Num. all: 33688 / Num. obs: 33688 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rpim(I) all: 0.051 / Rrim(I) all: 0.129 / Rsym value: 0.118 / Net I/av σ(I): 4.066 / Net I/σ(I): 8 / Num. measured all: 212948
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.216.30.6611.13091749080.2880.6612.6100
2.21-2.356.30.4231.82915146240.1830.4233.7100
2.35-2.516.30.2912.62780043830.1250.2914.9100
2.51-2.716.30.2243.22562240480.0960.2246.3100
2.71-2.976.40.1694.12380937470.0720.1698.1100
2.97-3.326.40.1384.72164634000.0590.13810.7100
3.32-3.836.40.1185.41895629790.050.11813.3100
3.83-4.76.40.0976.51617525470.0420.09715.4100
4.7-6.646.30.07981255619840.0340.07914.4100
6.64-44.5635.90.0619.6631610680.0270.06116.697.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DB9

4db9


Resolution: 2.1→44.563 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 1707 5.07 %
Rwork0.1722 --
obs0.1761 33653 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.41 Å2 / Biso mean: 52.1719 Å2 / Biso min: 27.36 Å2
Refinement stepCycle: final / Resolution: 2.1→44.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4282 0 8 233 4523
Biso mean--59.7 51.61 -
Num. residues----578
Refinement TLS params.Method: refined / Origin x: -10.3339 Å / Origin y: -10.4321 Å / Origin z: -57.6838 Å
111213212223313233
T0.3392 Å20.079 Å20.0472 Å2-0.3306 Å2-0.0439 Å2--0.3626 Å2
L0.4558 °2-0.2472 °20.2749 °2-0.492 °2-0.2358 °2--1.1396 °2
S-0.074 Å °-0.0653 Å °-0.1069 Å °-0.0534 Å °-0.0692 Å °0.1011 Å °0.1663 Å °-0.1679 Å °0.1219 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 291
2X-RAY DIFFRACTION1allB3 - 291
3X-RAY DIFFRACTION1allW1 - 282
4X-RAY DIFFRACTION1allC1 - 9
5X-RAY DIFFRACTION1allC10 - 11

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