[English] 日本語
Yorodumi
- PDB-1s7o: Crystal structure of putative DNA binding protein SP_1288 from St... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s7o
TitleCrystal structure of putative DNA binding protein SP_1288 from Streptococcus pygenes
ComponentsHypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Putative DNA binding protein / Signal recognition particle / RNA polymerase Sigma Factor / X-Rat crystallography / UPF0122 / structure funded by NIH / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


Putative helix-turn-helix protein, YlxM/p13-like / Putative helix-turn-helix protein, YlxM / p13 like / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
UPF0122 protein SpyM3_0842 / UPF0122 protein SPy_1201/M5005_Spy0916
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsOganesyan, V. / Pufan, R. / DeGiovanni, A. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the putative DNA-binding protein SP_1288 from Streptococcus pyogenes.
Authors: Oganesyan, V. / Pufan, R. / DeGiovanni, A. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionJan 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152
B: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152
C: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152


Theoretical massNumber of molelcules
Total (without water)40,8133
Polymers40,8133
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152
C: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152


Theoretical massNumber of molelcules
Total (without water)27,2092
Polymers27,2092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-20 kcal/mol
Surface area12560 Å2
MethodPISA, PQS
3
A: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152

A: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152


Theoretical massNumber of molelcules
Total (without water)27,2092
Polymers27,2092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)127.608, 69.685, 55.247
Angle α, β, γ (deg.)90.00, 103.04, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is probably dimer; molecules with chain identifiers B and C

-
Components

#1: Protein Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152


Mass: 13604.293 Da / Num. of mol.: 3 / Fragment: gi 15675166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M3 (bacteria)
Species: Streptococcus pyogenes / Strain: serotype M3 / Gene: SPY1201, SPYM3_0842, SPS1042, SPYM18_1152 / Plasmid: pB3.1325B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P67253, UniProt: P0DG80*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.19 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.2
Details: Citric Acid, Ammonium Nitrate, pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2003 / Details: Mirrors
RadiationMonochromator: Double-crystal, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→38 Å / Num. all: 40688 / Num. obs: 40607 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4 / Num. unique all: 4066 / Rsym value: 0.336 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5refinement
Blu-Icedata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→38.35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.301 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.281 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23686 1053 5.1 %RANDOM
Rwork0.20651 ---
all0.2081 19476 --
obs0.2081 19476 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.264 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å2-0.4 Å2
2--2.2 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.31→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 0 103 2794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222731
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9523688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6283315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00715498
X-RAY DIFFRACTIONr_chiral_restr0.10.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022082
X-RAY DIFFRACTIONr_nbd_refined0.2540.31237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.379
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.516
X-RAY DIFFRACTIONr_mcbond_it0.861.51587
X-RAY DIFFRACTIONr_mcangle_it1.74322568
X-RAY DIFFRACTIONr_scbond_it3.03831144
X-RAY DIFFRACTIONr_scangle_it5.0054.51120
LS refinement shellResolution: 2.308→2.368 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 61 -
Rwork0.224 1321 -
obs-1360 99.8 %
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)
14.82152.2332.83894.65594.39266.45620.1383-0.46680.06170.2855-0.08170.20010.1256-0.2581-0.05660.0392-0.01240.02720.09610.01770.0757.836544.360842.2744
23.8237-0.1634-1.34216.72281.06480.65690.0568-0.3721-0.17690.3477-0.18190.0312-0.03090.27260.12510.0384-0.002-0.04010.14520.02420.076558.57916.518832.2443
30.87521.03221.64582.21333.594911.9206-0.0462-0.19140.0581-0.0039-0.0748-0.0289-0.2271-0.21980.1210.08680.0366-0.00260.0721-0.00450.043385.822814.216749.8748
43.21520.43581.07231.8264-1.60962.8289-0.0081-0.17090.30610.2409-0.02480.2716-0.2017-0.06240.03290.06480.03620.03830.0583-0.03360.102279.067623.943223.5662
52.0745-1.9137-0.78755.97370.36342.21060.020.0949-0.1245-0.1908-0.06050.24920.1557-0.32310.04050.0571-0.0247-0.01210.10420.010.05578.8301-9.785431.6162
62.9860.87670.12323.1696-1.83941.3892-0.17110.3443-0.3006-0.14640.28680.21550.058-0.1017-0.11570.0596-0.0078-0.00940.0982-0.0340.076676.869615.873116.7497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 747 - 74
2X-RAY DIFFRACTION2AA75 - 11175 - 111
3X-RAY DIFFRACTION3BB6 - 746 - 74
4X-RAY DIFFRACTION4BB75 - 11075 - 110
5X-RAY DIFFRACTION5CC5 - 745 - 74
6X-RAY DIFFRACTION6CC75 - 11175 - 111

+
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