[English] 日本語
Yorodumi
- PDB-5c34: Constitutively active Sin recombinase cataltyic domain - I100T/Q115R -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c34
TitleConstitutively active Sin recombinase cataltyic domain - I100T/Q115R
ComponentsPutative transposon Tn552 DNA-invertase bin3
KeywordsDNA BINDING PROTEIN / Serine recombinase / Site specific recombinase / Conformational flexibility
Function / homology
Function and homology information


transposition / DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function
Resolvase, N-terminal catalytic domain / Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain ...Resolvase, N-terminal catalytic domain / Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative transposon Tn552 DNA-invertase bin3
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.655 Å
AuthorsTrejo, C.S. / Rice, P.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)T32EB009412 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM086826 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM078450 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Snapshots of a molecular swivel in action
Authors: Trejo, C.S. / Rock, R.S. / Star, W.M. / Boocock, M.R. / Rice, P.A.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Putative transposon Tn552 DNA-invertase bin3
C: Putative transposon Tn552 DNA-invertase bin3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6535
Polymers30,3652
Non-polymers2883
Water362
1
B: Putative transposon Tn552 DNA-invertase bin3
C: Putative transposon Tn552 DNA-invertase bin3
hetero molecules

B: Putative transposon Tn552 DNA-invertase bin3
C: Putative transposon Tn552 DNA-invertase bin3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,30610
Polymers60,7304
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area6410 Å2
ΔGint-153 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.010, 74.010, 181.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-201-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 1 - 124 / Label seq-ID: 1 - 124

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain BBA
2chain CCB

-
Components

#1: Protein Putative transposon Tn552 DNA-invertase bin3


Mass: 15182.423 Da / Num. of mol.: 2 / Fragment: UNP residues 1-128 / Mutation: R54E, I100T, Q115R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: bin3 / Production host: Escherichia coli (E. coli) / References: UniProt: P20384
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10mM DTT, 50mM HEPES, pH 7.0, 1.92 M AmSO4, 8% PEG 400, 10% propylene glycol

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 9886 / % possible obs: 98.6 % / Redundancy: 12.5 % / Biso Wilson estimate: 76.54 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.028 / Rrim(I) all: 0.098 / Χ2: 2.821 / Net I/av σ(I): 40.792 / Net I/σ(I): 10.1 / Num. measured all: 123147
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.57-2.618.64280.5420.50.69488.4
2.61-2.66104620.6320.4370.76395.9
2.66-2.7111.64770.6670.3850.75898.8
2.71-2.77134770.870.260.7451000.9270.964
2.77-2.8313.44900.9040.2110.73199.40.7660.796
2.83-2.8913.34770.9220.1740.7571000.6220.647
2.89-2.9713.65000.9540.1210.7781000.4420.459
2.97-3.0513.14800.9740.0920.8181000.330.343
3.05-3.1413.34830.9860.0690.8671000.2510.261
3.14-3.2413.54900.9890.0590.8921000.2170.225
3.24-3.3513.24980.9920.0451.031000.1620.168
3.35-3.4913.34930.9960.0371.1711000.1320.137
3.49-3.65134930.9980.0271.32899.80.0960.1
3.65-3.8413.24970.9980.0231.57699.60.0830.086
3.84-4.0813.15060.9990.0191.96999.40.070.073
4.08-4.3912.84930.9990.0172.59999.40.0610.063
4.39-4.8412.65140.9990.0194.23999.20.0680.07
4.84-5.5312.35120.9980.0226.048990.0790.082
5.53-6.9711.75350.9980.02712.21798.90.0970.101
6.97-5010.35810.9970.02316.46194.80.0810.085

-
Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIX(phenix.refine: dev_1951)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PKZ

3pkz


Resolution: 2.655→36.263 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3066 472 5.19 %
Rwork0.2932 8619 -
obs0.294 9091 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 253.91 Å2 / Biso mean: 127.2255 Å2 / Biso min: 57 Å2
Refinement stepCycle: final / Resolution: 2.655→36.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 15 2 1953
Biso mean--115.48 99.54 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041969
X-RAY DIFFRACTIONf_angle_d0.7652642
X-RAY DIFFRACTIONf_chiral_restr0.04305
X-RAY DIFFRACTIONf_plane_restr0.002335
X-RAY DIFFRACTIONf_dihedral_angle_d12.341771
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1323X-RAY DIFFRACTION5.804TORSIONAL
12C1323X-RAY DIFFRACTION5.804TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6548-3.03880.35771290.358427972926100
3.0388-3.82790.3921660.34528272993100
3.8279-36.2660.27391770.26412995317299

+
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