[English] 日本語
Yorodumi
- PDB-6p5t: Surface-layer (S-layer) RsaA protein from Caulobacter crescentus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p5t
TitleSurface-layer (S-layer) RsaA protein from Caulobacter crescentus bound to strontium and iodide
ComponentsS-layer protein
KeywordsMEMBRANE PROTEIN / surface array / self-assembling / coat protein / RTX motif
Function / homology
Function and homology information


S-layer / calcium ion binding / extracellular region
Similarity search - Function
RsaA N-terminal domain / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
IODIDE ION / STRONTIUM ION / S-layer protein
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChan, A.C. / Herrmann, J. / Smit, J. / Wakatsuki, S. / Murphy, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2015-04802 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly.
Authors: Herrmann, J. / Li, P.N. / Jabbarpour, F. / Chan, A.C.K. / Rajkovic, I. / Matsui, T. / Shapiro, L. / Smit, J. / Weiss, T.M. / Murphy, M.E.P. / Wakatsuki, S.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
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.ptnr3_auth_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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-layer protein
B: S-layer protein
C: S-layer protein
D: S-layer protein
E: S-layer protein
F: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)490,318280
Polymers460,4176
Non-polymers29,900274
Water87,1394837
1
B: S-layer protein
D: S-layer protein
E: S-layer protein
hetero molecules

A: S-layer protein
C: S-layer protein
F: S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)490,318280
Polymers460,4176
Non-polymers29,900274
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y+1/2,-z+21
Unit cell
Length a, b, c (Å)210.729, 80.564, 221.833
Angle α, β, γ (deg.)90.000, 117.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 251 through 287 or resid 289...
21(chain B and (resid 251 through 287 or resid 289...
31(chain C and (resid 251 through 287 or resid 289...
41(chain D and (resid 251 through 287 or resid 289...
51(chain E and (resid 251 through 287 or resid 289...
61(chain F and (resid 251 through 287 or resid 289...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain A and (resid 251 through 287 or resid 289...AA251 - 28739 - 75
12GLYGLYILEILE(chain A and (resid 251 through 287 or resid 289...AA289 - 31377 - 101
13GLYGLYSERSER(chain A and (resid 251 through 287 or resid 289...AA315 - 452103 - 240
14THRTHRALAALA(chain A and (resid 251 through 287 or resid 289...AA454 - 1026242 - 814
21THRTHRLEULEU(chain B and (resid 251 through 287 or resid 289...BB251 - 28739 - 75
22GLYGLYILEILE(chain B and (resid 251 through 287 or resid 289...BB289 - 31377 - 101
23GLYGLYSERSER(chain B and (resid 251 through 287 or resid 289...BB315 - 452103 - 240
24THRTHRALAALA(chain B and (resid 251 through 287 or resid 289...BB454 - 1026242 - 814
31THRTHRLEULEU(chain C and (resid 251 through 287 or resid 289...CC251 - 28739 - 75
32GLYGLYILEILE(chain C and (resid 251 through 287 or resid 289...CC289 - 31377 - 101
33GLYGLYSERSER(chain C and (resid 251 through 287 or resid 289...CC315 - 452103 - 240
34THRTHRALAALA(chain C and (resid 251 through 287 or resid 289...CC454 - 1026242 - 814
41THRTHRLEULEU(chain D and (resid 251 through 287 or resid 289...DD251 - 28739 - 75
42GLYGLYILEILE(chain D and (resid 251 through 287 or resid 289...DD289 - 31377 - 101
43GLYGLYSERSER(chain D and (resid 251 through 287 or resid 289...DD315 - 452103 - 240
44THRTHRALAALA(chain D and (resid 251 through 287 or resid 289...DD454 - 1026242 - 814
51THRTHRLEULEU(chain E and (resid 251 through 287 or resid 289...EE251 - 28739 - 75
52GLYGLYILEILE(chain E and (resid 251 through 287 or resid 289...EE289 - 31377 - 101
53GLYGLYSERSER(chain E and (resid 251 through 287 or resid 289...EE315 - 452103 - 240
54THRTHRALAALA(chain E and (resid 251 through 287 or resid 289...EE454 - 1026242 - 814
61THRTHRLEULEU(chain F and (resid 251 through 287 or resid 289...FF251 - 28739 - 75
62GLYGLYILEILE(chain F and (resid 251 through 287 or resid 289...FF289 - 31377 - 101
63GLYGLYSERSER(chain F and (resid 251 through 287 or resid 289...FF315 - 452103 - 240
64THRTHRALAALA(chain F and (resid 251 through 287 or resid 289...FF454 - 1026242 - 814

-
Components

#1: Protein
S-layer protein / Paracrystalline surface layer protein


Mass: 76736.203 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: rsaA, CC_1007 / Production host: Escherichia coli (E. coli) / References: UniProt: P35828
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 150 / Source method: obtained synthetically / Formula: I
#3: Chemical...
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 124 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4837 / 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: 3.63 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 8.5% PEG 8000, 100 mM Tris-HCl, 150 mM strontium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→49.3 Å / Num. obs: 384732 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.1 / Rrim(I) all: 0.25 / Net I/σ(I): 8.1 / Num. measured all: 2446368 / Scaling rejects: 1483
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.145.51.834100730183720.6180.8392.0251.396.8
11.5-49.35.80.0571450624920.9970.0250.06229.898.6

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N8P

5n8p


Resolution: 2.1→49.3 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.67
RfactorNum. reflection% reflection
Rfree0.2427 19202 5 %
Rwork0.2055 --
obs0.2074 384015 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.75 Å2 / Biso mean: 38.5156 Å2 / Biso min: 3.09 Å2
Refinement stepCycle: final / Resolution: 2.1→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30881 0 274 4839 35994
Biso mean--48.25 35.49 -
Num. residues----4682
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A13860X-RAY DIFFRACTION6.097TORSIONAL
12B13860X-RAY DIFFRACTION6.097TORSIONAL
13C13860X-RAY DIFFRACTION6.097TORSIONAL
14D13860X-RAY DIFFRACTION6.097TORSIONAL
15E13860X-RAY DIFFRACTION6.097TORSIONAL
16F13860X-RAY DIFFRACTION6.097TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.3766140.3449117011231595
2.1239-2.14880.33886280.3261119181254699
2.1488-2.17510.35036400.31981215912799100
2.1751-2.20260.33136330.30561194912582100
2.2026-2.23160.3236410.2931222912870100
2.2316-2.26210.30166410.2791201312654100
2.2621-2.29450.31346340.28011219212826100
2.2945-2.32870.30676380.26731203212670100
2.3287-2.36510.28256460.26141223112877100
2.3651-2.40390.28246250.25151201312638100
2.4039-2.44530.31756430.251222512868100
2.4453-2.48980.31246480.24821207112719100
2.4898-2.53770.2756330.23741217512808100
2.5377-2.58950.2916330.23741213912772100
2.5895-2.64580.28016390.23271210412743100
2.6458-2.70730.28166480.22561218612834100
2.7073-2.7750.28186390.22051218012819100
2.775-2.850.26716330.2161210512738100
2.85-2.93390.25186320.20871213912771100
2.9339-3.02860.24486490.20711217212821100
3.0286-3.13680.24936410.20841218912830100
3.1368-3.26240.23246420.19371221912861100
3.2624-3.41080.21016410.18111220612847100
3.4108-3.59060.21596440.17291218512829100
3.5906-3.81550.19186430.16821227712920100
3.8155-4.10990.19976470.1681222212869100
4.1099-4.52330.18736440.14581229012934100
4.5233-5.17720.17446430.13891225112894100
5.1772-6.52030.2116530.17441239913052100
6.5203-49.31690.20326670.1831264213309100
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)
10.0033-0.0058-0.00330.0060.00470.002-0.038-0.02350.02240.0163-0.02210.03960.0403-0.0478-00.24830.00520.00450.1126-0.00720.2727120.289121.5863185.9875
20.0855-0.01860.06070.10.05570.04370.01250.0837-0.00590.0348-0.00030.08590.0350.14920.01750.197-0.03830.03040.00160.07010.2723144.03271.2883184.7985
30.0423-0.01930.0122-0.01380.01090.03060.03340.08430.0317-0.01-0.05140.021-0.04090.1989-00.1795-0.0342-0.00270.2950.01060.2561186.1016-9.848191.7912
40.07510.050.06090.03460.01070.06940.0083-0.12450.03940.01560.0172-0.0103-0.06020.044200.2108-0.01770.00280.40220.01120.2336189.9658-16.7599240.7558
50.00020.00210.00030.0053-0.00050.00090.0540.01590.0025-0.015-0.02210.02590.0217-0.095800.2020.0038-0.01560.1346-0.01350.2369131.572558.308186.3368
60.0884-0.0239-0.02520.01470.030.10920.0353-0.0029-0.0569-0.0150.0080.1091-0.00760.14760.01350.1710.00230.00120.10430.0060.2378152.150139.7085187.9184
70.0502-0.04130.00530.050.02030.01180.04330.0734-0.0591-0.0169-0.00980.0191-0.01590.169200.18390.0315-0.0090.3249-0.04930.2639191.587630.5502189.7038
80.0309-0.01190.04630.03850.07780.0915-0.0323-0.0692-0.0450.0548-0.03740.01430.0332-0.073100.26480.01880.03880.5713-0.01320.2714201.413923.2042240.682
90.28710.10060.15320.23710.09170.12170.04320.46440.0030.05-0.08960.02120.0264-0.0056-0.05280.16360.1097-0.01120.4845-0.05660.2218114.82882.4794144.4733
100.08070.0433-0.080.2088-0.04230.07210.02370.1665-0.14310.1505-0.1443-0.1792-0.121-0.1787-0.10330.25030.00150.09531.0601-0.22060.2465171.1522-16.2186129.557
110.2346-0.06560.07410.21320.07860.15810.02760.40910.01770.0695-0.07220.08990.031-0.0411-0.00150.14150.008-0.05050.4319-0.05590.1364126.602439.203145.257
120.079-0-0.02290.06580.1130.05790.0320.1374-0.01470.0349-0.0419-0.07630.011-0.1086-0.00180.2344-0.0013-0.00010.8062-0.00080.3372183.657521.2252133.0328
130.0540.11770.02940.106-0.02180.16160.0030.04780.0121-0.0174-0.0306-0.04510.0009-0.1787-0.00010.22490.014-0.02130.3334-0.02580.216976.636545.4275157.658
140.09690.1079-0.04590.0982-0.08270.1-0.1276-0.0024-0.0329-0.0179-0.0406-0.0614-0.00930.0601-0.04070.281-0.01330.01890.65830.07860.231694.066727.100598.7126
150.05690.11790.02240.04160.00060.1910.06910.0788-0.02810.01480.007-0.0480.0582-0.01580.02990.18780.0532-0.02320.2215-0.04860.178865.65484.5222154.4361
160.09920.1263-0.10210.1011-0.1570.1428-0.2117-0.0529-0.015-0.02860.0585-0.06350.04370.0711-0.00450.30630.01340.04840.5914-0.02590.231685.2487-14.208795.9088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 245 through 285 )A245 - 285
2X-RAY DIFFRACTION2chain 'A' and (resid 286 through 539 )A286 - 539
3X-RAY DIFFRACTION3chain 'A' and (resid 540 through 749 )A540 - 749
4X-RAY DIFFRACTION4chain 'A' and (resid 750 through 1026 )A750 - 1026
5X-RAY DIFFRACTION5chain 'B' and (resid 251 through 300 )B251 - 300
6X-RAY DIFFRACTION6chain 'B' and (resid 301 through 496 )B301 - 496
7X-RAY DIFFRACTION7chain 'B' and (resid 497 through 728 )B497 - 728
8X-RAY DIFFRACTION8chain 'B' and (resid 729 through 1026 )B729 - 1026
9X-RAY DIFFRACTION9chain 'C' and (resid 247 through 660 )C247 - 660
10X-RAY DIFFRACTION10chain 'C' and (resid 661 through 1026 )C661 - 1026
11X-RAY DIFFRACTION11chain 'D' and (resid 247 through 678 )D247 - 678
12X-RAY DIFFRACTION12chain 'D' and (resid 679 through 1026 )D679 - 1026
13X-RAY DIFFRACTION13chain 'E' and (resid 247 through 660 )E247 - 660
14X-RAY DIFFRACTION14chain 'E' and (resid 661 through 1026 )E661 - 1026
15X-RAY DIFFRACTION15chain 'F' and (resid 246 through 678 )F246 - 678
16X-RAY DIFFRACTION16chain 'F' and (resid 679 through 1026 )F679 - 1026

+
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