[English] 日本語
Yorodumi
- PDB-7f5y: Crystal structure of the single-stranded dna-binding protein from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f5y
TitleCrystal structure of the single-stranded dna-binding protein from Mycobacterium tuberculosis- Form III
ComponentsSingle-stranded DNA-binding protein
KeywordsDNA BINDING PROTEIN / DNA binding / quaternary structure / plasticity / inhibitor development
Function / homology
Function and homology information


nucleoid / single-stranded DNA binding / DNA replication / response to antibiotic / DNA damage response / extracellular region / plasma membrane
Similarity search - Function
Single-stranded DNA-binding protein / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
FORMIC ACID / Single-stranded DNA-binding protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSrikalaivani, R. / Paul, A. / Sriram, R. / Narayanan, S. / Gopal, B. / Vijayan, M.
Funding support India, 1items
OrganizationGrant numberCountry
Office of the Principal Scientific Adviser to the Government of India India
CitationJournal: Curr.Sci. / Year: 2022
Title: Structural variability of Mycobacterium tuberculosis SSB and susceptibility to inhibition.
Authors: Srikalaivani, R. / Paul, A. / Sriram, R. / Narayanan, S. / Shee, S. / Singh, A. / Varshney, U. / Gopal, B. / Vijayan, M.
History
DepositionJun 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3896
Polymers35,2052
Non-polymers1844
Water1,71195
1
A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules

A: Single-stranded DNA-binding protein
B: Single-stranded DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,77812
Polymers70,4094
Non-polymers3688
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area10830 Å2
ΔGint-55 kcal/mol
Surface area22220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.550, 59.550, 124.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-341-

HOH

31B-431-

HOH

41B-450-

HOH

-
Components

#1: Protein Single-stranded DNA-binding protein / SSB


Mass: 17602.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: ssb, Rv0054, MTCY21D4.17 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGD5
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.82 Å3/Da / Density % sol: 32.31 %
Crystal growTemperature: 295 K / Method: microbatch / Details: 3.5M sodium formate, 100mM bis-tris propane pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→39 Å / Num. obs: 18944 / % possible obs: 96.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.9
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2650 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UE1

1ue1


Resolution: 1.92→39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.835 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22864 974 5.1 %RANDOM
Rwork0.19124 ---
obs0.19328 17963 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.92→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 12 95 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0141739
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171541
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.6642367
X-RAY DIFFRACTIONr_angle_other_deg0.9261.6373584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7955233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41120.79588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67315262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4731517
X-RAY DIFFRACTIONr_chiral_restr0.0630.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02311
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_it3.723.961932
X-RAY DIFFRACTIONr_mcbond_other3.7183.96933
X-RAY DIFFRACTIONr_mcangle_it5.4645.8831165
X-RAY DIFFRACTIONr_mcangle_other5.4625.8881166
X-RAY DIFFRACTIONr_scbond_it4.684.356806
X-RAY DIFFRACTIONr_scbond_other4.6464.362803
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9556.3351203
X-RAY DIFFRACTIONr_long_range_B_refined9.08345.3521708
X-RAY DIFFRACTIONr_long_range_B_other9.09845.2751696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 91 -
Rwork0.276 1252 -
obs--93.78 %

+
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