[English] 日本語
Yorodumi
- PDB-5wtp: Crystal structure of the C-terminal domain of outer membrane prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wtp
TitleCrystal structure of the C-terminal domain of outer membrane protein A (OmpA) from Capnocytophaga gingivalis
ComponentsOmpA family protein
KeywordsMEMBRANE PROTEIN / prokaryote / TT3R / TSP / calcium-binding motif
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane / cell adhesion / calcium ion binding
Similarity search - Function
Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain ...Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 60s Ribosomal Protein L30; Chain: A; / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCapnocytophaga gingivalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDai, S. / Tan, K. / Ye, S. / Zhang, R.
CitationJournal: Cell Calcium / Year: 2017
Title: Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability.
Authors: Dai, S. / Sun, C. / Tan, K. / Ye, S. / Zhang, R.
History
DepositionDec 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OmpA family protein
B: OmpA family protein
C: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,12832
Polymers42,3423
Non-polymers2,78629
Water3,729207
1
A: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,17112
Polymers14,1141
Non-polymers1,05711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,97910
Polymers14,1141
Non-polymers8659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,97910
Polymers14,1141
Non-polymers8659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.366, 130.366, 56.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-509-

SO4

21C-654-

HOH

-
Components

#1: Protein OmpA family protein


Mass: 14114.091 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 335-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga gingivalis (bacteria) / Gene: CAPGI0001_0903 / Production host: Escherichia coli (E. coli) / References: UniProt: C2M2E7
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris-HCl, pH 8.0, 3 M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→48.191 Å / Num. obs: 26492 / % possible obs: 97.6 % / Redundancy: 5.1 % / Net I/σ(I): 7.1
Reflection shellResolution: 2.15→2.19 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FBY

3fby


Resolution: 2.15→48.191 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.27
RfactorNum. reflection% reflection
Rfree0.2332 1271 4.81 %
Rwork0.1819 --
obs0.1844 26425 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→48.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 145 207 3257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033061
X-RAY DIFFRACTIONf_angle_d0.7084104
X-RAY DIFFRACTIONf_dihedral_angle_d13.0341161
X-RAY DIFFRACTIONf_chiral_restr0.026429
X-RAY DIFFRACTIONf_plane_restr0.003521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1496-2.23570.28951450.21882679X-RAY DIFFRACTION96
2.2357-2.33740.29791240.21612723X-RAY DIFFRACTION96
2.3374-2.46070.27231410.20772735X-RAY DIFFRACTION96
2.4607-2.61480.2611510.21412726X-RAY DIFFRACTION97
2.6148-2.81670.28781280.20952726X-RAY DIFFRACTION96
2.8167-3.10010.24561460.18632812X-RAY DIFFRACTION99
3.1001-3.54860.23291410.17122815X-RAY DIFFRACTION98
3.5486-4.47030.18491490.14162871X-RAY DIFFRACTION99
4.4703-48.20310.2151460.18393067X-RAY DIFFRACTION99
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)
14.380.5349-0.22154.0679-2.18021.63040.11810.452-0.126-0.4491-0.13291.25360.23850.0242-0.27780.2190.02560.02990.22730.02520.500253.9549-31.685210.1924
22.7884-4.53772.63658.6435-1.98577.29980.22890.34940.1706-0.4539-0.2217-0.2997-0.07070.2298-0.00650.2619-0.01910.01720.24610.01710.183647.3432-20.14946.5627
31.15720.7285-1.63865.00962.41945.00540.36861.53171.1494-0.4919-0.75430.5542-0.0377-0.45920.01810.2030.1268-0.01520.46240.20830.312927.7772-16.88336.6432
48.7045-3.35693.47736.9589-3.54345.298-0.21761.20110.0159-1.0197-0.01160.029-0.13910.26080.08720.33870.0063-0.04840.3705-0.05930.248138.888-26.69141.2629
53.427-0.7141-0.53956.31030.73820.656-0.2279-0.1450.12260.47090.3109-0.16870.0535-0.0462-0.04050.20580.039-0.00890.17690.01490.153838.9871-21.579715.6096
62.6647-2.2024-2.32239.62645.91265.7051-0.14480.14240.0288-0.04460.03020.6185-0.07640.13660.09740.18240.0077-0.00570.23910.04270.163230.0241-22.211414.5707
72.5524-0.70750.96864.54471.86285.3817-0.0865-0.187-0.36490.26190.40160.18350.49780.216-0.39430.1783-0.00710.02370.2080.02480.166837.4651-29.110615.409
85.96960.7908-1.58472.9946-4.80177.97210.09530.08460.16210.753-0.4434-0.6738-0.4770.48320.34230.2045-0.0018-0.02640.1867-0.02220.281838.737-6.087718.1694
93.7916-1.7-0.62615.67741.310.85340.14690.17410.26610.1584-0.0947-0.2623-0.16320.1419-0.03020.15630.01410.01520.19540.02980.191339.6028-12.656212.1628
109.80947.16663.0065.23392.2281.13920.6824-0.52120.45110.5839-0.7441.3624-0.4175-1.1187-0.00730.40910.030.14080.44570.09650.63274.72-21.98623.946
112.41471.63030.94314.09770.7495.92660.7531-1.39350.48321.264-0.43220.5138-0.0519-0.5468-0.10750.654-0.07770.15950.3683-0.03470.34449.097-34.59820.482
122.69050.1635-2.06135.3506-0.4715.68670.3541-1.44610.15850.5794-0.5626-1.29260.06121.26830.03780.2966-0.0803-0.110.52830.13050.488724.581-41.05511.741
131.9752.81311.37594.61791.46882.19870.5647-0.8065-0.47121.4186-0.2251-0.51440.6778-0.0819-0.35020.51840.0018-0.05810.31550.08110.348312.22-31.9319.96
141.41581.16180.57723.7821-0.01941.1667-0.0569-0.03970.1405-0.0340.0920.19620.16270.00820.03490.17470.0190.0430.2226-0.00020.26520.25-31.72423.114
151.9573-0.03930.18712.09310.27891.36430.0029-0.1737-0.0193-0.0116-0.01650.04980.07660.0150.01610.1568-0.00560.01790.17550.01430.253324.186-33.63420.874
162.29522.9905-0.04574.64350.86730.8875-0.1294-0.0231-0.0940.06010.23160.1021-0.03130.2373-0.13230.1788-0.02470.03190.22630.0270.240517.927-40.81224.053
177.7668-5.8713-2.46144.78812.74114.4304-0.1552-0.7697-0.8730.28030.37191.03710.1693-1.0701-0.29190.3601-0.01190.00430.7930.22390.374946.548-56.66418.062
184.467-3.08895.24287.1193-2.12776.72570.61921.053-1.5419-0.8092-0.09880.16490.70440.7782-0.63650.51760.0332-0.03150.3839-0.08630.373467.832-53.36814.031
196.0788-3.6911-1.94318.24682.89664.15630.14740.3918-0.3872-0.7085-0.01370.81690.3917-1.26270.05890.3966-0.0497-0.14640.44190.05360.244456.508-63.54318.543
205.0006-0.90376.57262.3465-0.69588.8078-0.3719-0.45341.10250.29990.0020.06270.1629-0.73320.17610.24540.0970.00540.40110.05040.334744.524-64.8768.811
214.506-3.90722.77824.9008-3.13382.9606-0.2307-0.17760.23140.090.2314-0.83870.1428-0.4361-0.01880.22580.00440.02040.2729-0.00960.218358.209-46.8078.51
224.5015-2.11623.03284.0833-3.20473.40440.12240.28520.0429-0.2258-0.2628-0.24850.39440.1180.12150.25830.0020.03380.2026-0.03010.144362.474-53.9145.801
231.5686-0.318-1.01147.45041.51750.9605-0.3863-0.01080.05230.33330.31240.2455-0.6297-0.39290.13130.24920.05190.00380.32150.00370.176553.391-61.6344.781
246.32261.3704-1.66939.7861-1.51134.53430.4334-0.1919-0.44090.5309-0.1260.45370.5758-0.1843-0.17170.3934-0.0486-0.04930.31590.05420.229856.567-39.05611.559
253.5651-3.29061.22563.2262-0.40086.49840.01670.8612-0.9796-0.8141-0.30171.10430.8572-0.1560.13270.5402-0.1081-0.09450.3994-0.05520.416460.438-40.15119.348
265.7994-2.266-0.25537.247-1.60273.96410.18410.6676-0.0235-0.2238-0.08030.39880.3474-0.727-0.08040.2008-0.0014-0.01790.31280.04980.169752.888-51.41911.845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 331 through 337 )
2X-RAY DIFFRACTION2chain 'A' and (resid 338 through 350 )
3X-RAY DIFFRACTION3chain 'A' and (resid 351 through 361 )
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 377 )
5X-RAY DIFFRACTION5chain 'A' and (resid 378 through 394 )
6X-RAY DIFFRACTION6chain 'A' and (resid 395 through 415 )
7X-RAY DIFFRACTION7chain 'A' and (resid 416 through 429 )
8X-RAY DIFFRACTION8chain 'A' and (resid 430 through 439 )
9X-RAY DIFFRACTION9chain 'A' and (resid 440 through 454 )
10X-RAY DIFFRACTION10chain 'B' and (resid 334 through 337 )
11X-RAY DIFFRACTION11chain 'B' and (resid 338 through 350 )
12X-RAY DIFFRACTION12chain 'B' and (resid 351 through 361 )
13X-RAY DIFFRACTION13chain 'B' and (resid 362 through 377 )
14X-RAY DIFFRACTION14chain 'B' and (resid 378 through 394 )
15X-RAY DIFFRACTION15chain 'B' and (resid 395 through 439 )
16X-RAY DIFFRACTION16chain 'B' and (resid 440 through 454 )
17X-RAY DIFFRACTION17chain 'C' and (resid 334 through 350 )
18X-RAY DIFFRACTION18chain 'C' and (resid 351 through 361 )
19X-RAY DIFFRACTION19chain 'C' and (resid 362 through 377 )
20X-RAY DIFFRACTION20chain 'C' and (resid 378 through 382 )
21X-RAY DIFFRACTION21chain 'C' and (resid 383 through 394 )
22X-RAY DIFFRACTION22chain 'C' and (resid 395 through 415 )
23X-RAY DIFFRACTION23chain 'C' and (resid 416 through 427 )
24X-RAY DIFFRACTION24chain 'C' and (resid 428 through 439 )
25X-RAY DIFFRACTION25chain 'C' and (resid 440 through 446 )
26X-RAY DIFFRACTION26chain 'C' and (resid 447 through 454 )

+
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://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