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

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Basic information

Entry
Database: PDB / ID: 4plq
TitleCrystal Structures of Designed Armadillo Repeat Proteins: Implications of Construct Design and Crystallization Conditions on Overall Structure.
ComponentsArm00011
KeywordsPEPTIDE BINDING PROTEIN / designed armadillo repeat protein / 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
AuthorsMittl, P.R. / Reichen, C. / Madhurantakam, C. / Pluckthun, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationS-41105-06-01 Switzerland
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 2.0Sep 13, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_validate_symm_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_audit_support.funding_organization / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2
Revision 2.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arm00011


Theoretical massNumber of molelcules
Total (without water)29,6451
Polymers29,6451
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.530, 105.040, 55.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Arm00011


Mass: 29645.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: artificial sequence / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4 M Sodium citrate, 0.1 M HEPES

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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: May 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.12 Å / Num. obs: 16190 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 43.264 Å2 / Rmerge F obs: 0.091 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.068 / Χ2: 1.015 / Net I/σ(I): 18.19 / Num. measured all: 102543
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.20.5490.6223.113209208120790.67899.9
2.2-2.30.4150.4664.6811190172017000.50798.8
2.3-2.40.2250.2587.189892146514650.28100
2.4-2.50.20.2168.588255122812270.23499.9
2.5-2.70.1460.1611.1312769195419540.174100
2.7-30.080.09117.4412314204220410.1100
3-40.0350.0530.5820260324132350.05599.8
4-70.0220.03540.1511593199319790.03899.3
70.0150.02545.7430615175100.02898.6

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4plr

4plr


Resolution: 2.1→49.12 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.858 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 813 5 %RANDOM
Rwork0.1997 15340 --
obs0.2028 16153 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.26 Å2 / Biso mean: 41.424 Å2 / Biso min: 18.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.1→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 0 57 2143
Biso mean---40.27 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192110
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9812879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9565283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.91429.25594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.83315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.085151
X-RAY DIFFRACTIONr_chiral_restr0.1460.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211603
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 59 -
Rwork0.269 1013 -
all-1072 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -19.0269 Å / Origin y: -16.5996 Å / Origin z: 16.4114 Å
111213212223313233
T0.0618 Å20.0037 Å20.0033 Å2-0.0704 Å20.0152 Å2--0.0234 Å2
L0.5467 °20.2517 °2-0.2389 °2-0.9904 °2-0.0733 °2--0.2423 °2
S-0.1053 Å °-0.0667 Å °-0.0049 Å °-0.1062 Å °0.1069 Å °-0.0695 Å °0.0658 Å °0.0068 Å °-0.0015 Å °

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