[English] 日本語
Yorodumi
- PDB-7w7i: Crystal Structure of shaft pilin PitB from pilus islet-2 of Strep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w7i
TitleCrystal Structure of shaft pilin PitB from pilus islet-2 of Streptococcus oralis
ComponentsFctA domain-containing protein
KeywordsCELL ADHESION / Shaft pilin / adhesin / PitB / PI-2 pilus / Streptococcus oralis / isopeptide / omega loop / dental plaque / biofilm
Function / homologyStreptococcal pilin isopeptide linker / Streptococcal pilin isopeptide linker superfamily / Spy0128-like isopeptide containing domain / membrane => GO:0016020 / FctA domain-containing protein
Function and homology information
Biological speciesStreptococcus oralis ATCC 35037 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsYadav, R.K. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2019/000432 India
CitationJournal: Febs J. / Year: 2022
Title: New structural insights into the PI-2 pilus from Streptococcus oralis, an early dental plaque colonizer.
Authors: Yadav, R.K. / Krishnan, V.
History
DepositionDec 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Derived calculations / Category: atom_type / citation
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: FctA domain-containing protein
B: FctA domain-containing protein
C: FctA domain-containing protein
D: FctA domain-containing protein
E: FctA domain-containing protein
F: FctA domain-containing protein
G: FctA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)268,9357
Polymers268,9357
Non-polymers00
Water28816
1
A: FctA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)38,4191
Polymers38,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FctA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)38,4191
Polymers38,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FctA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)38,4191
Polymers38,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FctA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)38,4191
Polymers38,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: FctA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)38,4191
Polymers38,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: FctA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)38,4191
Polymers38,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: FctA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)38,4191
Polymers38,4191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.629, 34.530, 207.516
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTHRTHRAA33 - 37412 - 353
21ASNASNTHRTHRBB33 - 37412 - 353
12ASPASPTHRTHRAA34 - 37413 - 353
22ASPASPTHRTHRCC34 - 37413 - 353
13ALAALATHRTHRAA36 - 37415 - 353
23ALAALATHRTHRDD36 - 37415 - 353
14THRTHRTHRTHRAA37 - 37416 - 353
24THRTHRTHRTHREE37 - 37416 - 353
15ASPASPTHRTHRAA34 - 37413 - 353
25ASPASPTHRTHRFF34 - 37413 - 353
16ALAALAVALVALAA36 - 37315 - 352
26ALAALAVALVALGG36 - 37315 - 352
17ASPASPPROPROBB34 - 37513 - 354
27ASPASPPROPROCC34 - 37513 - 354
18ALAALAPROPROBB36 - 37515 - 354
28ALAALAPROPRODD36 - 37515 - 354
19THRTHRPROPROBB37 - 37516 - 354
29THRTHRPROPROEE37 - 37516 - 354
110ASPASPTHRTHRBB34 - 37413 - 353
210ASPASPTHRTHRFF34 - 37413 - 353
111ALAALAVALVALBB36 - 37315 - 352
211ALAALAVALVALGG36 - 37315 - 352
112ALAALAPROPROCC36 - 37515 - 354
212ALAALAPROPRODD36 - 37515 - 354
113THRTHRPROPROCC37 - 37516 - 354
213THRTHRPROPROEE37 - 37516 - 354
114ASPASPTHRTHRCC34 - 37413 - 353
214ASPASPTHRTHRFF34 - 37413 - 353
115ALAALAVALVALCC36 - 37315 - 352
215ALAALAVALVALGG36 - 37315 - 352
116THRTHRPROPRODD37 - 37516 - 354
216THRTHRPROPROEE37 - 37516 - 354
117ALAALATHRTHRDD36 - 37415 - 353
217ALAALATHRTHRFF36 - 37415 - 353
118ALAALATHRTHRDD36 - 37415 - 353
218ALAALATHRTHRGG36 - 37415 - 353
119THRTHRTHRTHREE37 - 37416 - 353
219THRTHRTHRTHRFF37 - 37416 - 353
120THRTHRTHRTHREE37 - 37416 - 353
220THRTHRTHRTHRGG37 - 37416 - 353
121ALAALATHRTHRFF36 - 37415 - 353
221ALAALATHRTHRGG36 - 37415 - 353

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

-
Components

#1: Protein
FctA domain-containing protein / PitB shaft pilin


Mass: 38419.281 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus oralis ATCC 35037 (bacteria)
Gene: HMPREF8579_1186 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D4FSQ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8
Details: 100 mM Bis-Tris pH 8.0, 200 mM zinc acetate dihydrate, and 20% PEG smear medium

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 3.591→49.603 Å / Num. obs: 19653 / % possible obs: 84.3 % / Redundancy: 3.1 % / CC1/2: 0.956 / Rpim(I) all: 0.186 / Net I/σ(I): 4 / % possible ellipsoidal: 84.3 / % possible spherical: 56.2
Reflection shellResolution: 3.591→3.758 Å / Redundancy: 2.9 % / Num. unique obs: 837 / CC1/2: 0.696 / Rpim(I) all: 0.502 / % possible all: 88.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F7Y

7f7y


Resolution: 3.59→49.6 Å / Cor.coef. Fo:Fc: 0.759 / Cor.coef. Fo:Fc free: 0.697 / SU B: 190.364 / SU ML: 1.226 / Cross valid method: THROUGHOUT / ESU R Free: 1.495 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The completeness within the ellipsoidal limits is 84.3%.
RfactorNum. reflection% reflectionSelection details
Rfree0.358 939 4.8 %RANDOM
Rwork0.32 ---
obs0.322 18713 56.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.81 Å2
Baniso -1Baniso -2Baniso -3
1--3.54 Å20 Å2-4.22 Å2
2--0.95 Å20 Å2
3---3 Å2
Refinement stepCycle: LAST / Resolution: 3.59→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16643 0 0 16 16659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01116940
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.65522947
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39952361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21925.458535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.797152251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4951511
X-RAY DIFFRACTIONr_chiral_restr0.1040.22490
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212637
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4453.0619486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6534.58111833
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0173.0497454
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.83656.1366777
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85590.16
12B85590.16
21A84070.18
22C84070.18
31A85200.16
32D85200.16
41A82710.17
42E82710.17
51A85150.17
52F85150.17
61A81540.18
62G81540.18
71B85780.16
72C85780.16
81B86690.17
82D86690.17
91B84210.17
92E84210.17
101B85140.18
102F85140.18
111B81690.18
112G81690.18
121C85030.18
122D85030.18
131C83000.18
132E83000.18
141C84710.18
142F84710.18
151C81710.18
152G81710.18
161D83830.17
162E83830.17
171D85830.17
172F85830.17
181D82880.17
182G82880.17
191E83480.17
192F83480.17
201E80220.19
202G80220.19
211F83220.18
212G83220.18
LS refinement shellResolution: 3.59→3.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 22 -
Rwork0.424 427 -
obs--17.72 %
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)
16.0586-0.05582.10470.027-0.08431.0353-0.14720.1896-0.05770.0284-0.01660.02090.00150.06020.16390.39880.08030.06830.2525-0.22630.4988-292.5746-24.5983-56.7323
23.79080.44621.73090.34330.0260.9182-0.02820.4550.0048-0.0190.0776-0.0172-0.02710.1787-0.04930.45850.02270.19970.4462-0.01990.2412-209.4863-25.7657-21.1309
34.36930.47361.26880.34190.32220.6973-0.09980.0587-0.20390.04850.102-0.0134-0.18480.0945-0.00220.4745-0.13850.16290.37380.10110.304743.69512.41866.3464
43.05920.85281.25180.2980.26321.07560.19870.0331-0.1951-0.0457-0.0913-0.11090.1280.1473-0.10730.46560.05680.0310.20720.06570.5668-129.4237-19.635819.7312
53.60470.95311.32530.31440.36590.6086-0.01160.0967-0.181-0.030.1691-0.0825-0.092-0.0291-0.15750.259-0.15940.09840.5532-0.00680.4546211.236533.6014126.565
63.57340.70070.8920.24960.16660.2541-0.28710.1924-0.1428-0.00120.25450.0967-0.11290.09430.03260.246-0.11240.12350.64690.25930.4344-44.2762-2.818145.7462
74.92381.29461.61570.55660.32261.0768-0.71-0.0848-0.5263-0.36640.3794-0.2516-0.263-0.06820.33050.2736-0.33510.07430.7396-0.0690.4973128.190513.079797.2855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 375
2X-RAY DIFFRACTION2B33 - 376
3X-RAY DIFFRACTION3C34 - 376
4X-RAY DIFFRACTION4D36 - 376
5X-RAY DIFFRACTION5E37 - 376
6X-RAY DIFFRACTION6F34 - 375
7X-RAY DIFFRACTION7G36 - 374

+
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