[English] 日本語
Yorodumi
- PDB-5mfd: Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5 -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more