[English] 日本語
Yorodumi
- PDB-3zqm: Crystal structure of the small terminase oligomerization core dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zqm
TitleCrystal structure of the small terminase oligomerization core domain from a SPP1-like bacteriophage (crystal form 1)
ComponentsTERMINASE SMALL SUBUNIT
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / MOLECULAR MOTOR / DNA PACKAGING
Function / homology
Function and homology information


chromosome organization / DNA binding / identical protein binding
Similarity search - Function
Helix Hairpins - #2160 / Terminase small subunit / Terminase small subunit, N-terminal DNA-binding domain, HTH motif superfamily / Terminase small subunit / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Terminase small subunit / Terminase small subunit
Similarity search - Component
Biological speciesBACILLUS PHAGE SF6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsButtner, C.R. / Chechik, M. / Ortiz-Lombardia, M. / Smits, C. / Chechik, V. / Jeschke, G. / Dykeman, E. / Benini, S. / Alonso, J.C. / Antson, A.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Basis for DNA Recognition and Loading Into a Viral Packaging Motor.
Authors: Buttner, C.R. / Chechik, M. / Ortiz-Lombardia, M. / Smits, C. / Ebong, I.O. / Chechik, V. / Jeschke, G. / Dykeman, E. / Benini, S. / Robinson, C.V. / Alonso, J.C. / Antson, A.A.
History
DepositionJun 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Other
Revision 1.2Feb 15, 2012Group: Other

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TERMINASE SMALL SUBUNIT
B: TERMINASE SMALL SUBUNIT
C: TERMINASE SMALL SUBUNIT
D: TERMINASE SMALL SUBUNIT
E: TERMINASE SMALL SUBUNIT
F: TERMINASE SMALL SUBUNIT
G: TERMINASE SMALL SUBUNIT
H: TERMINASE SMALL SUBUNIT
I: TERMINASE SMALL SUBUNIT
J: TERMINASE SMALL SUBUNIT


Theoretical massNumber of molelcules
Total (without water)80,67110
Polymers80,67110
Non-polymers00
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21850 Å2
ΔGint-146.4 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.954, 60.009, 81.442
Angle α, β, γ (deg.)90.00, 100.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
TERMINASE SMALL SUBUNIT / SF6 SMALL TERMINASE G1P / G1P


Mass: 8067.110 Da / Num. of mol.: 10 / Fragment: OLIGOMERIZATION CORE DOMAIN, RESIDUES 53-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS PHAGE SF6 (virus) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q1EJR8, UniProt: P68928*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 58 % / Description: NONE
Crystal growDetails: 0.1 M MALONATE/IMIDAZOLE/BORIC ACID BUFFER SYSTEM PH 7.0, 25 % PEG 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.971557
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971557 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 52842 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.3 / % possible all: 86

-
Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.85→80.06 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.286 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21351 2644 5.1 %RANDOM
Rwork0.17175 ---
obs0.17389 49111 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.483 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.09 Å2
2---0.7 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.85→80.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4367 0 0 421 4788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224395
X-RAY DIFFRACTIONr_bond_other_d0.0010.023075
X-RAY DIFFRACTIONr_angle_refined_deg1.5812.0055862
X-RAY DIFFRACTIONr_angle_other_deg0.91937658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4585564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45226.471170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17815984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.551520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024707
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02681
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 160 -
Rwork0.211 3026 -
obs--83.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.9572-0.9806-4.37250.83771.94245.4271-0.00220.02780.0072-0.04220.1725-0.0902-0.1080.2851-0.17040.1993-0.0241-0.08920.32980.02550.350334.23260.51173.614
20.6719-0.57260.59311.2966-0.74851.265-0.1588-0.07520.10030.00120.0447-0.2857-0.179-0.06630.11410.3099-0.0099-0.04950.21770.01150.317918.21374.80466.836
32.3085-2.71681.88983.7806-1.31853.04730.0588-0.01590.0279-0.0725-0.1242-0.06810.165-0.18940.06540.2762-0.0039-0.02980.2796-0.00180.300118.44758.25877.759
44.4688-1.8148-2.06290.75460.6483.0451-0.3231-0.54830.22720.18230.2257-0.118-0.38340.09870.09750.32330.0263-0.13280.2723-0.03290.271520.28561.83887.279
50.4607-0.4192-0.21321.4256-1.131.8387-0.1121-0.07320.17320.13280.1596-0.1019-0.0774-0.0521-0.04740.32490.0139-0.10280.22050.00650.30628.4575.48273.16
63.6496-3.17934.02825.3403-3.00324.54930.1064-0.12580.0968-0.1008-0.1715-0.24360.1566-0.20660.0650.29830.0028-0.01920.3027-0.00860.25468.24656.95881.651
710.71291.20832.29610.45310.23220.5040.1472-0.88760.09740.1585-0.14170.0943-0.0154-0.2193-0.00550.33930.00490.0090.39020.00490.15935.05159.10291.208
80.48620.17560.18672.2522-1.6071.3725-0.2506-0.0990.11440.00420.1187-0.0256-0.1322-0.20810.13190.29150.0322-0.04640.2795-0.03910.2977-2.77271.63673.839
91.8494-0.24371.79334.7479-5.94478.7713-0.1428-0.1197-0.0572-0.2182-0.0743-0.29710.3235-0.19230.21710.3598-0.0563-0.01250.33230.02040.225-1.42152.2580.046
104.16271.65.47880.62982.173610.15150.0448-0.4913-0.03590.0223-0.1273-0.01210.0603-0.79220.08240.2944-0.08980.10030.41870.02630.1548-9.67151.485.065
110.1717-0.27450.46083.1204-1.34671.5899-0.1166-0.07650.06840.11850.02280.0502-0.0737-0.31290.09380.28270.0026-0.02890.3189-0.01710.2721-11.52866.8968.454
120.2023-0.4717-0.184.1148-2.98516.2192-0.10150.19250.07280.1999-0.1129-0.27590.3612-0.17190.21440.3381-0.07180.04870.320.00750.218-7.0947.3871.471
131.8203-0.3054-1.56560.64452.24558.0013-0.1052-0.0824-0.04530.088-0.15930.08790.2685-0.36510.26460.3443-0.20550.18750.2915-0.08240.2056-16.69343.40472.55
140.0564-0.1518-0.2233.93180.07721.0122-0.01680.0467-0.0247-0.1076-0.15110.17780.0044-0.14930.16790.24130.0018-0.03550.3088-0.03280.2853-13.85260.79858.52
150.39581.2808-0.96596.845-1.91633.0446-0.01150.00430.02570.2786-0.0494-0.07770.2616-0.05210.06090.3242-0.04230.02440.3005-0.02030.2611-6.81441.8462.043
160.03880.1458-0.01562.20112.1152.9045-0.0126-0.0492-0.02750.1316-0.41210.20910.2096-0.18770.42470.3346-0.08830.030.3009-0.04450.2615-12.33437.6654.785
170.03660.0554-0.05931.4550.61790.7178-0.007-0.0493-0.0551-0.2838-0.09350.1458-0.1357-0.05570.10050.31240.0544-0.02560.28570.00370.2614-10.31960.20748.747
181.37282.4431-0.82737.9284-2.90051.30090.042-0.1118-0.09680.0242-0.128-0.20910.01510.08890.0860.2902-0.00010.01020.27570.02610.27850.09640.7553.162
191.04430.7067-0.44061.1270.52091.24070.08090.1689-0.16630.1682-0.007-0.22410.1561-0.1647-0.07390.28740.03210.00140.2687-0.03260.3201-1.58535.62844.097
201.0863-0.37630.17491.57070.2840.1207-0.0684-0.1309-0.1475-0.40340.12180.0146-0.14640.0208-0.05340.37310.02830.02540.27960.04550.2124-1.48559.48142.109
213.91130.5995-0.990910.4737-0.19260.2988-0.1684-0.3746-0.07970.10670.310.09560.02010.1527-0.14160.17610.06530.05770.3221-0.04760.391810.14541.97549.469
229.21866.52270.02458.68393.17292.4504-0.34550.2977-0.1193-0.35730.618-0.4219-0.07120.2999-0.27250.21030.1064-0.0260.3143-0.06960.356815.74838.64641.74
230.7841-0.71550.11113.0570.49310.1652-0.19350.0745-0.0682-0.47470.2793-0.1806-0.19650.099-0.08580.3152-0.04720.09990.30390.06120.241910.90560.44740.92
241.9711.50310.50787.60351.07441.39510.17840.1126-0.14690.11630.38980.02950.04260.3473-0.56830.13350.05320.03260.3049-0.08460.384819.91946.12852.094
252.01452.55711.174.5584.48057.5196-0.11360.2636-0.1225-0.08210.5575-0.30960.08630.6671-0.44390.04130.0949-0.01190.466-0.24650.396628.02445.31445.507
261.5647-0.95780.61952.14750.19790.4917-0.13430.15930.1176-0.27770.2165-0.216-0.21630.2377-0.08220.2355-0.13320.09140.31880.02320.313119.56565.76746.381
272.9481-2.95810.083510.50861.3990.3013-0.38140.373-0.42450.32510.47570.219-0.04660.1761-0.09430.18080.00060.09430.3417-0.08160.374525.59151.5259.675
282.97281.32051.80363.42062.98142.7734-0.03960.3035-0.2069-0.1790.3442-0.3364-0.16410.3307-0.30450.092-0.0040.03930.3932-0.06690.42535.6753.61260.325
291.4694-0.56991.42790.6012-0.22421.7166-0.16190.00470.1705-0.06020.1289-0.2291-0.18070.1680.0330.2774-0.09350.02010.2693-0.00250.329222.14170.98456.721
302.8857-2.75040.32153.2222-1.68453.25560.0459-0.08260.0351-0.11030.13620.0020.1958-0.0402-0.18210.1929-0.0074-0.03150.3012-0.03260.349325.70555.72969.787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A62 - 79
2X-RAY DIFFRACTION2A80 - 107
3X-RAY DIFFRACTION3A108 - 120
4X-RAY DIFFRACTION4B65 - 80
5X-RAY DIFFRACTION5B81 - 107
6X-RAY DIFFRACTION6B108 - 120
7X-RAY DIFFRACTION7C64 - 80
8X-RAY DIFFRACTION8C81 - 108
9X-RAY DIFFRACTION9C109 - 120
10X-RAY DIFFRACTION10D65 - 80
11X-RAY DIFFRACTION11D81 - 107
12X-RAY DIFFRACTION12D108 - 120
13X-RAY DIFFRACTION13E64 - 80
14X-RAY DIFFRACTION14E81 - 108
15X-RAY DIFFRACTION15E109 - 120
16X-RAY DIFFRACTION16F65 - 84
17X-RAY DIFFRACTION17F85 - 107
18X-RAY DIFFRACTION18F108 - 120
19X-RAY DIFFRACTION19G63 - 84
20X-RAY DIFFRACTION20G85 - 107
21X-RAY DIFFRACTION21G108 - 120
22X-RAY DIFFRACTION22H66 - 80
23X-RAY DIFFRACTION23H81 - 107
24X-RAY DIFFRACTION24H108 - 120
25X-RAY DIFFRACTION25I63 - 80
26X-RAY DIFFRACTION26I81 - 107
27X-RAY DIFFRACTION27I108 - 120
28X-RAY DIFFRACTION28J65 - 80
29X-RAY DIFFRACTION29J81 - 108
30X-RAY DIFFRACTION30J109 - 120

+
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