[English] 日本語
Yorodumi
- PDB-5xlk: Crystal structure of the flagellar cap protein FliD D2-D3 domains... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xlk
TitleCrystal structure of the flagellar cap protein FliD D2-D3 domains from Serratia marcescens in Space group I422
ComponentsFlagellar hook-associated protein 2
KeywordsSTRUCTURAL PROTEIN / Bacterial flagellar cap protein
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / cell adhesion / extracellular region
Similarity search - Function
Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin hook, IN motif / Flagellin hook IN motif
Similarity search - Domain/homology
Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsCho, S.Y. / Song, W.S. / Hong, H.J. / Yoon, S.I.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Tetrameric structure of the flagellar cap protein FliD from Serratia marcescens.
Authors: Cho, S.Y. / Song, W.S. / Hong, H.J. / Lee, G.S. / Kang, S.G. / Ko, H.J. / Kim, P.H. / Yoon, S.I.
History
DepositionMay 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar hook-associated protein 2
B: Flagellar hook-associated protein 2
C: Flagellar hook-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,04912
Polymers65,4603
Non-polymers5899
Water00
1
A: Flagellar hook-associated protein 2
B: Flagellar hook-associated protein 2
hetero molecules

A: Flagellar hook-associated protein 2
B: Flagellar hook-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06516
Polymers87,2804
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area7330 Å2
ΔGint-301 kcal/mol
Surface area33690 Å2
MethodPISA
2
C: Flagellar hook-associated protein 2
hetero molecules

C: Flagellar hook-associated protein 2
hetero molecules

C: Flagellar hook-associated protein 2
hetero molecules

C: Flagellar hook-associated protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06516
Polymers87,2804
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area7460 Å2
ΔGint-317 kcal/mol
Surface area32390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.362, 121.362, 249.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11C-301-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A79 - 103
2113B79 - 103
3113C79 - 103
1213A226 - 299
2213B226 - 299
3213C226 - 299
1123A104 - 199
2123B104 - 199
3123C104 - 199
1223A203 - 225
2223B203 - 225
3223C203 - 225

NCS ensembles :
ID
1
2

-
Components

#1: Protein Flagellar hook-associated protein 2 / HAP2 / Flagellar cap protein


Mass: 21820.078 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 71-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: AR325_17470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0QFX8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.5 M sodium chloride, 0.1 M imidazole, pH 8.0, and 0.2 M zinc acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. obs: 17805 / % possible obs: 96.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 25.9
Reflection shellResolution: 3.05→3.1 Å / Rmerge(I) obs: 0.476

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XLJ

5xlj


Resolution: 3.05→30 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.84 / SU B: 35.096 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 1.913 / ESU R Free: 0.441 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28654 841 4.8 %RANDOM
Rwork0.23841 ---
obs0.24069 16662 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 47.564 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.8 Å2
Refinement stepCycle: 1 / Resolution: 3.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3998 0 9 0 4007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224030
X-RAY DIFFRACTIONr_bond_other_d0.0020.022473
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9635496
X-RAY DIFFRACTIONr_angle_other_deg0.90436168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.19427.152151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76715641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0611514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024593
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02653
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3581.52794
X-RAY DIFFRACTIONr_mcbond_other0.0731.51145
X-RAY DIFFRACTIONr_mcangle_it0.74324465
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51731236
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6864.51031
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A408tight positional0.020.05
11B408tight positional0.030.05
11C408tight positional0.030.05
22A665tight positional0.030.05
22B665tight positional0.030.05
22C665tight positional0.040.05
11A329loose positional0.035
11B329loose positional0.035
11C329loose positional0.035
22A650loose positional0.035
22B650loose positional0.035
22C650loose positional0.045
11A408tight thermal0.040.5
11B408tight thermal0.050.5
11C408tight thermal0.050.5
22A665tight thermal0.060.5
22B665tight thermal0.060.5
22C665tight thermal0.060.5
11A329loose thermal0.0610
11B329loose thermal0.0510
11C329loose thermal0.0610
22A650loose thermal0.0610
22B650loose thermal0.0610
22C650loose thermal0.0710
LS refinement shellResolution: 3.05→3.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 59 -
Rwork0.303 1223 -
obs--98.69 %
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)
19.87841.5577-7.2395.0070.683411.64410.0634-0.1363-0.03110.5072-0.42940.26660.8172-0.96330.3660.231-0.12610.01080.2507-0.04090.146-48.208-14.49513.982
24.7452-0.1798-0.19743.1442-0.89533.57170.04210.50790.134-0.2099-0.0818-0.2406-0.13840.10750.03960.07210.03350.020.06850.03840.0793-24.763-10.304-10.897
315.7596-1.26327.53675.47681.52287.81340.41111.1649-0.8165-0.2552-0.46220.61740.0759-0.02190.05110.14540.0378-0.00030.2724-0.12510.2023-74.744-14.38912.609
44.83580.7461-0.26452.9862-0.63365.6310.0415-0.21910.20120.1965-0.1807-0.1685-0.08770.52010.13920.0567-0.0339-0.01320.06710.0080.0604-49.824-10.36135.881
513.9253-5.18051.04996.45941.50365.56880.39361.0574-1.57280.08850.00770.16670.3170.4981-0.40140.11750.0666-0.12280.2281-0.18790.4804-46.742-48.18148.046
62.9509-0.3263-0.78755.0204-0.53023.235-0.0734-0.1432-0.07240.17460.10220.3489-0.2505-0.1341-0.02880.09340.01990.07250.05960.01980.0569-71.43-24.71250.743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 103
2X-RAY DIFFRACTION1A226 - 269
3X-RAY DIFFRACTION2A104 - 225
4X-RAY DIFFRACTION3B79 - 103
5X-RAY DIFFRACTION3B226 - 269
6X-RAY DIFFRACTION4B104 - 225
7X-RAY DIFFRACTION5C79 - 103
8X-RAY DIFFRACTION5C226 - 269
9X-RAY DIFFRACTION6C104 - 225

+
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