[English] 日本語
Yorodumi
- PDB-2eky: Crystal Structure of hypothetical protein MJ1052 from Methanocald... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2eky
TitleCrystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii (Form 1)
ComponentsUPF0045 protein MJ1052
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyThiamine-binding protein / : / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / UPF0045 protein MJ1052
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii
Authors: Mizutani, H. / Kunishima, N.
History
DepositionMar 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0045 protein MJ1052
B: UPF0045 protein MJ1052
C: UPF0045 protein MJ1052
D: UPF0045 protein MJ1052
E: UPF0045 protein MJ1052
F: UPF0045 protein MJ1052
G: UPF0045 protein MJ1052
H: UPF0045 protein MJ1052


Theoretical massNumber of molelcules
Total (without water)89,9468
Polymers89,9468
Non-polymers00
Water13,169731
1
A: UPF0045 protein MJ1052
B: UPF0045 protein MJ1052
C: UPF0045 protein MJ1052
D: UPF0045 protein MJ1052


Theoretical massNumber of molelcules
Total (without water)44,9734
Polymers44,9734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-50 kcal/mol
Surface area15750 Å2
MethodPISA, PQS
2
E: UPF0045 protein MJ1052
F: UPF0045 protein MJ1052
G: UPF0045 protein MJ1052
H: UPF0045 protein MJ1052


Theoretical massNumber of molelcules
Total (without water)44,9734
Polymers44,9734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-53 kcal/mol
Surface area15420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.437, 61.394, 87.811
Angle α, β, γ (deg.)90.00, 108.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
UPF0045 protein MJ1052


Mass: 11243.202 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q58452
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7
Details: 50%(v/v) PEG200, 0.1M Tris, pH 7.0, microbatch, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS VII1IMAGE PLATEFeb 5, 2007mirrors
RIGAKU RAXIS VII2IMAGE PLATEFeb 26, 2007mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 68040 / Num. obs: 68040 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.065 / Net I/σ(I): 9.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3.3 / Num. unique all: 6325 / Rsym value: 0.439 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LXN

1lxn


Resolution: 1.8→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1648422.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3418 5 %RANDOM
Rwork0.192 ---
all0.194 67958 --
obs0.192 67958 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.0032 Å2 / ksol: 0.357144 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å2-2.1 Å2
2--0.58 Å20 Å2
3---1.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6130 0 0 731 6861
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 541 5 %
Rwork0.233 10221 -
obs--94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.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