[English] 日本語
Yorodumi
- PDB-6x6o: Crystal structure of T4 protein Spackle as determined by native S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x6o
TitleCrystal structure of T4 protein Spackle as determined by native SAD phasing
ComponentsProtein spackle
KeywordsVIRAL PROTEIN / APOBEC / deaminase / HYDROLASE
Function / homologyProtein spackle / superinfection exclusion / host cell periplasmic space / Protein spackle
Function and homology information
Biological speciesEscherichia virus T4
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsShi, K. / Kurniawan, F. / Banerjee, S. / Moeller, N.H. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystal structure of bacteriophage T4 Spackle as determined by native SAD phasing.
Authors: Shi, K. / Kurniawan, F. / Banerjee, S. / Moeller, N.H. / Aihara, H.
History
DepositionMay 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein spackle
B: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2936
Polymers24,1522
Non-polymers1424
Water2,468137
1
A: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1824
Polymers12,0761
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein spackle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1112
Polymers12,0761
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.424, 79.822, 93.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-203-

CL

21A-344-

HOH

31B-357-

HOH

41B-369-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 23 through 61 or resid 63 through 95))
21(chain B and (resid 23 through 61 or resid 63 through 95))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 23 through 61 or resid 63 through 95))A23 - 61
121(chain A and (resid 23 through 61 or resid 63 through 95))A63 - 95
211(chain B and (resid 23 through 61 or resid 63 through 95))B23 - 61
221(chain B and (resid 23 through 61 or resid 63 through 95))B63 - 95

-
Components

#1: Protein Protein spackle


Mass: 12075.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus T4 / Gene: sp, 61.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P39230
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.71 Å3/Da / Density % sol: 28.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.5 M ammonium sulfate, 0.05 M sodium acetate buffer, pH 4.5, and 4 % (v/v) glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→60.7 Å / Num. obs: 47113 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 1 / Rmerge(I) obs: 0.033 / Net I/σ(I): 29.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 9 % / Rmerge(I) obs: 1.471 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1310 / CC1/2: 0.647 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→40.104 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 2299 4.88 %
Rwork0.1733 44813 -
obs0.1742 47112 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.51 Å2 / Biso mean: 42.881 Å2 / Biso min: 21.76 Å2
Refinement stepCycle: final / Resolution: 1.52→40.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 4 138 1354
Biso mean--84.51 45.25 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091236
X-RAY DIFFRACTIONf_angle_d0.9981663
X-RAY DIFFRACTIONf_dihedral_angle_d17.316773
X-RAY DIFFRACTIONf_chiral_restr0.057181
X-RAY DIFFRACTIONf_plane_restr0.007219
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A692X-RAY DIFFRACTION10.127TORSIONAL
12B692X-RAY DIFFRACTION10.127TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.52-1.55310.3681450.3626279695
1.5531-1.58920.29921150.3353277494
1.5892-1.62890.35641450.3139281696
1.6289-1.6730.37571490.3094281196
1.673-1.72220.32131470.2916279096
1.7222-1.77780.30191600.284273594
1.7778-1.84130.28551360.2373273594
1.8413-1.9150.22161680.2142285197
1.915-2.00220.24171380.2028279497
2.0022-2.10780.20471510.1812288596
2.1078-2.23980.20731570.1604276496
2.2398-2.41270.21261330.1619280295
2.4127-2.65550.18911290.1543274294
2.6555-3.03960.17241240.1638292598
3.0396-3.82910.16271310.1501285097
3.8291-40.1040.14821710.1516274394
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)
14.1609-4.5833-5.69135.21665.67619.1963-0.23580.0290.15040.24380.1222-0.2332-0.1015-0.22820.22460.18330.0072-0.04040.34060.00830.306118.7519.37416.824
27.8726-5.4265-1.60364.20182.01623.433-0.2701-0.37760.41320.48110.2085-0.52910.0046-0.11750.06180.2640.0379-0.07060.425-0.02620.318727.324.30726.099
33.50523.09472.32753.14380.79955.16320.30010.2033-0.2828-0.1143-0.0899-0.77210.32520.8062-0.29320.28450.0651-0.05950.5428-0.02050.441338.8552.80828.822
44.02841.31533.34483.10490.9865.4862-0.1041-0.22010.41290.308-0.0943-0.3989-0.13890.08980.11590.21770.0065-0.06150.3792-0.01840.443429.3729.87318.633
53.03230.6262-2.81573.0953-0.73213.65880.37741.1160.0407-0.603-0.7826-0.4907-0.04690.36950.37780.22640.0385-0.00440.4328-0.01040.308729.0223.25210.141
66.87746.30845.37248.28234.02024.5553-0.2690.13330.4052-0.14790.6663-1.1673-0.2861.0422-0.34120.20620.0091-0.03730.5063-0.10150.444836.4911.88918.634
76.2613-3.5026-3.53942.74313.85198.90810.06260.10860.3497-0.05420.117-0.37530.08420.285-0.1950.1928-0.00540.02470.3790.01380.36248.76723.34537.556
81.0417-1.3075-0.65683.692.15812.13890.00690.0292-0.15980.0097-0.0290.07420.2954-0.2060.05720.1642-0.0044-0.02830.3761-0.01270.294439.75414.11841.77
93.73621.2712-1.68112.5254-0.26232.40720.11990.0767-0.15980.0477-0.10970.6450.4304-1.1764-0.06390.2737-0.0768-0.01520.5965-0.03290.517928.29711.18241.902
102.08180.80210.80038.75014.08775.38050.1850.2876-0.0458-0.1543-0.10490.0820.1396-0.1644-0.04280.15710.0068-0.01030.3930.01870.310237.96821.70236.209
114.8568-5.07470.21977.26881.70723.07870.33940.23330.7842-0.03440.1705-0.051-0.5104-0.5561-0.42880.20860.00630.03430.35450.00050.3637.93330.00942.98
122.2751-0.51230.79970.2625-0.72392.4003-0.06970.08860.14120.0265-0.04981.1689-0.1495-0.8305-0.14510.19390.03880.00670.5588-0.02830.620727.33121.87943.407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 23:36 )A23 - 36
2X-RAY DIFFRACTION2( CHAIN A AND RESID 37:55 )A37 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:70 )A56 - 70
4X-RAY DIFFRACTION4( CHAIN A AND RESID 71:80 )A71 - 80
5X-RAY DIFFRACTION5( CHAIN A AND RESID 81:86 )A81 - 86
6X-RAY DIFFRACTION6( CHAIN A AND RESID 87:95 )A87 - 95
7X-RAY DIFFRACTION7( CHAIN B AND RESID 23:36 )B23 - 36
8X-RAY DIFFRACTION8( CHAIN B AND RESID 37:55 )B37 - 55
9X-RAY DIFFRACTION9( CHAIN B AND RESID 56:70 )B56 - 70
10X-RAY DIFFRACTION10( CHAIN B AND RESID 71:80 )B71 - 80
11X-RAY DIFFRACTION11( CHAIN B AND RESID 81:86 )B81 - 86
12X-RAY DIFFRACTION12( CHAIN B AND RESID 87:98 )B87 - 98

+
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