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- PDB-5mfd: Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 -

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Basic information

Entry
Database: PDB / ID: 5mfd
TitleDesigned armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5
Components
  • Capsid decoration protein,pD_(KR)5
  • YIIIM''6AII
KeywordsDE NOVO PROTEIN / Designed armadillo repeat protein / peptide binding
Function / homology
Function and homology information


viral capsid, decoration / viral DNA genome packaging / host cell cytoplasm
Similarity search - Function
Virus Head Decoration Protein; Chain: A, / Head decoration protein D / Head decoration protein D superfamily / Head decoration protein D / Bacteriophage lambda head decoration protein D / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Capsid decoration protein
Similarity search - Component
Biological speciessynthetic construct (others)
Enterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHansen, S. / Kiefer, J. / Madhurantakam, C. / Mittl, P. / Plueckthun, A.
CitationJournal: Protein Sci. / Year: 2017
Title: Structures of designed armadillo repeat proteins binding to peptides fused to globular domains.
Authors: Hansen, S. / Kiefer, J.D. / Madhurantakam, C. / Mittl, P.R.E. / Pluckthun, A.
History
DepositionNov 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 25, 2018Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.3Jan 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 / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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

Downloads & links

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Assembly

Deposited unit
A: YIIIM''6AII
B: Capsid decoration protein,pD_(KR)5
C: YIIIM''6AII
D: Capsid decoration protein,pD_(KR)5
E: YIIIM''6AII
F: Capsid decoration protein,pD_(KR)5
G: YIIIM''6AII
H: Capsid decoration protein,pD_(KR)5
I: YIIIM''6AII
J: YIIIM''6AII
K: YIIIM''6AII
L: YIIIM''6AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,70661
Polymers320,74212
Non-polymers1,96449
Water8,737485
1
A: YIIIM''6AII
B: Capsid decoration protein,pD_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,15310
Polymers45,8322
Non-polymers3218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: YIIIM''6AII
D: Capsid decoration protein,pD_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8723
Polymers45,8322
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: YIIIM''6AII
F: Capsid decoration protein,pD_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,23312
Polymers45,8322
Non-polymers40110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: YIIIM''6AII
H: Capsid decoration protein,pD_(KR)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,23312
Polymers45,8322
Non-polymers40110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: YIIIM''6AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5145
Polymers34,3531
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
J: YIIIM''6AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5145
Polymers34,3531
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
K: YIIIM''6AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,75411
Polymers34,3531
Non-polymers40110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
L: YIIIM''6AII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4333
Polymers34,3531
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)194.660, 194.660, 241.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
YIIIM''6AII


Mass: 34353.270 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Protein
Capsid decoration protein,pD_(KR)5 / Auxiliary protein D / Gene product D / gpD / Major capsid protein D


Mass: 11479.043 Da / Num. of mol.: 4 / Fragment: UNP residues 21-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: D, lambdap07 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03712
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 4.12 Å3/Da / Density % sol: 70.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28.0%v/v PEG 400, 0.2M Calcium chloride, 0.1M Na HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2395 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2395 Å / Relative weight: 1
ReflectionResolution: 2.1→49.12 Å / Num. obs: 300594 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 60.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.23 / Net I/σ(I): 8.45
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.149 / Mean I/σ(I) obs: 0.24 / CC1/2: 0.084 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCZ and 5AEI

1tcz

5aei


Resolution: 2.3→49.12 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.149 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.214 11555 5.05 %RANDOM
Rwork0.19 ---
obs0.191 228790 99.8 %-
Displacement parametersBiso mean: 76.08 Å2
Baniso -1Baniso -2Baniso -3
1--7.8016 Å20 Å20 Å2
2---7.8016 Å20 Å2
3---15.6033 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.3→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22206 0 49 485 22740
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00922583HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1130774HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7893SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes848HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3135HARMONIC5
X-RAY DIFFRACTIONt_it22583HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.07
X-RAY DIFFRACTIONt_other_torsion19.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3077SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact26854SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 904 5.44 %
Rwork0.251 15722 -
all0.252 16626 -
obs--98.1 %
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)
10.15560.26410.82971.69771.5282.1394-0.33240.2677-0.0775-0.64670.34050.0374-0.48310.6744-0.00810.1804-0.47650.02840.04140.0087-0.2901-55.12256.7333-123.825
20.1094-0.64991.53732.6234-3.3082.10460.2989-0.0717-0.1673-0.1805-0.20290.13330.63360.0807-0.0960.152-0.07550.0325-0.0121-0.0012-0.1141-65.117971.1848-143.283
30.63390.20.8520.53440.85432.2057-0.0094-0.03280.0497-0.0363-0.04780.01020.08220.05330.05720.0322-0.2340.0194-0.0434-0.0003-0.1165-64.39749.1714-101.029
4-0.3433-0.5462-1.26522.9222.23123.8727-0.17030.13230.02960.03130.2470.1710.35940.046-0.0767-0.0629-0.0523-0.09560.09730.0109-0.0963-76.290169.2647-82.9667
51.4789-0.5009-0.59140.4501-0.08591.3474-0.033-0.3390.04510.09640.04150.0674-0.19230.0645-0.0084-0.1619-0.0035-0.01950.133-0.0447-0.1639-74.042291.2789-41.3138
62.398-1.75211.96321.3466-3.47454.0682-0.14530.0360.06120.08880.18440.0011-0.3464-0.2552-0.039-0.12650.0295-0.11570.2144-0.0928-0.1148-67.59675.3529-21.6222
70.88720.07940.93110.33930.78762.48870.1231-0.2752-0.02070.1965-0.15890.03410.4806-0.60380.0358-0.1019-0.20780.01850.18560.0182-0.2149-58.793454.767719.3369
8-0.55580.54251.4225.5162.66443.0287-0.0420.0304-0.1432-0.00160.07430.32210.20410-0.0323-0.1884-0.2788-0.02770.17840.210.0363-68.771373.190838.3103
91.01760.3288-1.02750.3588-0.37562.5083-0.10110.1779-0.0039-0.04240.0446-0.0639-0.0073-0.26230.0565-0.19120.03920.00340.13760.0069-0.1238-86.00189.3282-63.9953
100.11150.36970.42581.02650.89052.827-0.08060.1093-0.0489-0.03540.02120.14990.1028-0.01830.0594-0.1991-0.1335-0.02860.1440.0043-0.1179-49.68363.0871-3.5104
110.7051-0.0949-0.60790.22020.072.39160.0003-0.0347-0.04340.0168-0.03210.1125-0.0504-0.15520.0317-0.1685-0.10910.00560.10750.0027-0.0688-66.221893.593280.1327
120.47420.5528-0.82690.7559-0.44122.3437-0.12890.37690.0516-0.11220.10930.03760.1385-0.690.0196-0.2342-0.1621-0.02250.26050.0007-0.1477-78.099992.007857.3424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }

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