[English] 日本語
Yorodumi
- PDB-1ni5: Structure of the MesJ PP-ATPase from Escherichia Coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ni5
TitleStructure of the MesJ PP-ATPase from Escherichia Coli
ComponentsPutative cell cycle protein mesJ
KeywordsCELL CYCLE / STRUCTURAL GENOMICS / ATPase / PP-type / putative cell cycle protein / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


tRNA wobble base lysidine biosynthesis / tRNAIle-lysidine synthase / tRNA(Ile)-lysidine synthase activity / tRNA modification / ATP binding / identical protein binding / cytosol
Similarity search - Function
Lysidine-tRNA(Ile) synthetase, C-terminal / tRNA(Ile)-lysidine synthase , substrate-binding domain / TilS substrate binding domain / TilS substrate C-terminal domain / TilS substrate C-terminal domain / Chorismate Mutase Domain, subunit A - #20 / tRNA(Ile)-lysidine synthase / tRNA(Ile)-lysidine synthase, N-terminal / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop family ...Lysidine-tRNA(Ile) synthetase, C-terminal / tRNA(Ile)-lysidine synthase , substrate-binding domain / TilS substrate binding domain / TilS substrate C-terminal domain / TilS substrate C-terminal domain / Chorismate Mutase Domain, subunit A - #20 / tRNA(Ile)-lysidine synthase / tRNA(Ile)-lysidine synthase, N-terminal / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop family / Chorismate Mutase Domain, subunit A / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
tRNA(Ile)-lysidine synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsGu, M. / Burling, T. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of the MesJ PP-ATPase from Escherichia coli
Authors: Gu, M. / Burling, T. / Lima, C.D.
History
DepositionDec 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative cell cycle protein mesJ


Theoretical massNumber of molelcules
Total (without water)48,5781
Polymers48,5781
Non-polymers00
Water3,477193
1
A: Putative cell cycle protein mesJ

A: Putative cell cycle protein mesJ


Theoretical massNumber of molelcules
Total (without water)97,1552
Polymers97,1552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3650 Å2
ΔGint-31 kcal/mol
Surface area43240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.508, 67.508, 204.678
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological dimer is generated by: ROTATION MATRIX -0.49997 0.86604 -0.00004 0.86604 0.49997 -0.00005 -0.00002 -0.00006 -1.00000 TRANSLATION VECTOR 0.00004 0.00071 0.00376

-
Components

#1: Protein Putative cell cycle protein mesJ


Mass: 48577.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MESJ / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 (DE3) / References: UniProt: P52097
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.5M MgFormate, pH unbuffered, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.65→20 Å / Num. all: 16421 / Num. obs: 16208 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.4
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1603 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→19.49 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 831 5.1 %RANDOM
Rwork0.223 ---
obs0.223 16208 98.7 %-
all-16421 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.872 Å2 / ksol: 0.295514 e/Å3
Displacement parametersBiso mean: 58.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å211.98 Å20 Å2
2--3.87 Å20 Å2
3----7.74 Å2
Refine analyzeLuzzati coordinate error free: 0.45 Å / Luzzati sigma a free: 0.62 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 0 193 3600
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.522
X-RAY DIFFRACTIONc_mcangle_it2.682.5
X-RAY DIFFRACTIONc_scbond_it1.792.5
X-RAY DIFFRACTIONc_scangle_it2.863
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.394 90 5.8 %
Rwork0.346 1456 -
obs-1546 96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
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