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- PDB-5mfn: Designed armadillo repeat protein YIIIM5AII -

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Basic information

Entry
Database: PDB / ID: 5mfn
TitleDesigned armadillo repeat protein YIIIM5AII
ComponentsYIIIM5AII
KeywordsDE NOVO PROTEIN / Designed armadillo repeat protein / peptide binding
Function / homologyD-MALATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHansen, S. / Ernst, P. / Reichen, C. / Ewald, C. / Mittl, P. / Plueckthun, A.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Curvature of designed armadillo repeat proteins allows modular peptide binding.
Authors: Hansen, S. / Ernst, P. / Konig, S.L.B. / Reichen, C. / Ewald, C. / Nettels, D. / Mittl, P.R.E. / Schuler, B. / Pluckthun, A.
History
DepositionNov 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YIIIM5AII
B: YIIIM5AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4437
Polymers60,0552
Non-polymers3885
Water28816
1
A: YIIIM5AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2023
Polymers30,0271
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YIIIM5AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2424
Polymers30,0271
Non-polymers2143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.550, 142.550, 142.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein YIIIM5AII


Mass: 30027.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.47 Å3/Da / Density % sol: 64.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Sodium malonate 2.4M pH 7.0, 0.2M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→46.66 Å / Num. obs: 21564 / % possible obs: 99.9 % / Redundancy: 39.7 % / Biso Wilson estimate: 89.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.257 / Net I/σ(I): 18.68
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 37.4 % / Rmerge(I) obs: 7.643 / Mean I/σ(I) obs: 0.69 / CC1/2: 0.184 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MFC

5mfc


Resolution: 2.8→46.66 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.517 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.523 / SU Rfree Blow DPI: 0.299 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1030 4.78 %RANDOM
Rwork0.2 ---
obs0.203 21564 100 %-
Displacement parametersBiso mean: 131.96 Å2
Baniso -1Baniso -2Baniso -3
1--17.9939 Å20 Å20 Å2
2---17.9939 Å20 Å2
3---35.9877 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: 1 / Resolution: 2.8→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4133 0 21 16 4170
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014193HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.325711HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1477SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes177HARMONIC2
X-RAY DIFFRACTIONt_gen_planes574HARMONIC5
X-RAY DIFFRACTIONt_it4193HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion24.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion568SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5292SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.268 134 4.8 %
Rwork0.244 2657 -
all0.245 2791 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.17180.4105-0.01972.0719-0.43893.3199-0.1204-0.27460.52370.3555-0.1626-0.7136-1.0760.78110.2830.3595-0.2149-0.1904-0.269-0.12810.119685.961-12.7425-13.3171
20.9707-0.6344-0.89452.4666-0.24414.6092-0.1254-0.59340.34121.3583-0.16980.6011-1.1507-1.05120.29510.52780.15430.15110.0918-0.407-0.134355.2344-16.60553.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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