[English] 日本語
Yorodumi
- PDB-5j1j: Structure of FleN-AMPPNP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j1j
TitleStructure of FleN-AMPPNP complex
ComponentsSite-determining protein
KeywordsTRANSCRIPTION / FleN / Antiactivator / AMPPNP
Function / homology
Function and homology information


cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Flagellum site-determining protein FlhG / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / ATP binding protein MinD/FleN / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Antiactivator FleN
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsJain, D. / Chanchal / Banerjee, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: Structure / Year: 2017
Title: ATP-Induced Structural Remodeling in the Antiactivator FleN Enables Formation of the Functional Dimeric Form
Authors: Chanchal / Banerjee, P. / Jain, D.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Site-determining protein
B: Site-determining protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,51011
Polymers60,9692
Non-polymers1,5419
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-112 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.050, 206.535, 103.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

21A-669-

HOH

31A-698-

HOH

41A-699-

HOH

51B-678-

HOH

61B-787-

HOH

-
Components

#1: Protein Site-determining protein


Mass: 30484.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: fleN / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XD64
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.34 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.26M ammonium sulphate, 0.1M sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 76475 / % possible obs: 99.9 % / Redundancy: 6 % / Net I/σ(I): 34
Reflection shellResolution: 1.55→1.58 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→37.25 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 3828 5.02 %
Rwork0.1697 --
obs0.1707 76182 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 89 572 4582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074134
X-RAY DIFFRACTIONf_angle_d1.1375646
X-RAY DIFFRACTIONf_dihedral_angle_d13.6031524
X-RAY DIFFRACTIONf_chiral_restr0.047679
X-RAY DIFFRACTIONf_plane_restr0.005715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5502-1.56980.24721280.22412515X-RAY DIFFRACTION95
1.5698-1.59050.21711420.212672X-RAY DIFFRACTION100
1.5905-1.61230.25141460.19712647X-RAY DIFFRACTION100
1.6123-1.63530.21991180.19292699X-RAY DIFFRACTION100
1.6353-1.65970.22811380.19272623X-RAY DIFFRACTION100
1.6597-1.68560.24571400.18652663X-RAY DIFFRACTION100
1.6856-1.71330.21041300.18012654X-RAY DIFFRACTION100
1.7133-1.74280.22361470.17562676X-RAY DIFFRACTION100
1.7428-1.77450.19211250.16672659X-RAY DIFFRACTION100
1.7745-1.80860.19421530.16422651X-RAY DIFFRACTION100
1.8086-1.84560.19231440.16712667X-RAY DIFFRACTION100
1.8456-1.88570.17361550.16222654X-RAY DIFFRACTION100
1.8857-1.92950.19951260.16282683X-RAY DIFFRACTION100
1.9295-1.97780.181410.16792667X-RAY DIFFRACTION100
1.9778-2.03130.19511660.16522651X-RAY DIFFRACTION100
2.0313-2.0910.18431450.16032666X-RAY DIFFRACTION100
2.091-2.15850.23841330.16462696X-RAY DIFFRACTION100
2.1585-2.23570.18491310.15572700X-RAY DIFFRACTION100
2.2357-2.32520.17841660.15832651X-RAY DIFFRACTION100
2.3252-2.4310.18741410.16342698X-RAY DIFFRACTION100
2.431-2.55910.18861430.16942680X-RAY DIFFRACTION100
2.5591-2.71940.16281390.1722735X-RAY DIFFRACTION100
2.7194-2.92930.21491470.17262682X-RAY DIFFRACTION100
2.9293-3.22390.17951490.17712725X-RAY DIFFRACTION100
3.2239-3.69010.17231520.1542730X-RAY DIFFRACTION100
3.6901-4.64770.15761440.15282756X-RAY DIFFRACTION100
4.6477-37.26110.20551390.19512854X-RAY DIFFRACTION98
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)
10.66220.1706-0.19620.82470.05980.63760.02430.02080.00850.0013-0.0229-0.0464-0.03620.0382-00.10750.0093-0.00210.11630.00680.094241.989288.320644.5117
20.73160.0768-0.13030.7706-0.1220.50740.0226-0.0494-0.0150.1027-0.0481-0.0565-0.03530.0299-0.00160.0926-0.0022-0.01250.08050.00740.087934.735566.573161.5052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 277)
2X-RAY DIFFRACTION2chain 'B' and (resid 8 through 255 )

+
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