[English] 日本語
Yorodumi
- PDB-4yte: N-terminal domain of HmdIII from Methanocaldococcus jannaschii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yte
TitleN-terminal domain of HmdIII from Methanocaldococcus jannaschii
ComponentsH(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ0715
KeywordsMETAL BINDING PROTEIN / Rossmann-like fold / [Fe]-hydrogenase paralog
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein / Methenyltetrahydromethanopterin dehydrogenase, Hmd-type / H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase, C-terminal / HMD, C-terminal domain superfamily / H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ0715
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
Funding support Japan, Germany, 2items
OrganizationGrant numberCountry
JST-PRESTO Japan
Max Planck Society Germany
CitationJournal: to be published
Title: N-terminal domain of HmdIII from Methanocaldococcus jannaschii
Authors: Fujishiro, T. / Kahnt, J. / Ermler, U. / Shima, S.
History
DepositionMar 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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: H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ0715


Theoretical massNumber of molelcules
Total (without water)21,2151
Polymers21,2151
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.780, 53.780, 127.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ0715


Mass: 21215.393 Da / Num. of mol.: 1 / Fragment: Rossmann-like domain, UNP residues 1-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0715 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58125
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20 % (w/v) PEG3350, 0.2M sodium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.971 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2014
RadiationMonochromator: A double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 12012 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 33.12 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.107 / Χ2: 0.886 / Net I/σ(I): 17.08 / Num. measured all: 99182
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.15-2.254.90.8510.6932.56702150513640.77590.6
2.25-2.40.9430.54.3812129181117580.54197.1
2.4-2.70.9760.3617.3423436258925880.383100
2.7-3.20.9930.19413.7921770243824370.206100
3.2-3.90.9990.08729.0215539167316720.09299.9
3.9-5.10.9990.04841.3710755116511650.051100
5.1-80.9990.04540.6165587357350.048100
8-1210.03552.1316061951950.037100
120.9990.03747.59687100980.0498

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-terminal domain of HmdII from M. jannaschii

Resolution: 2.15→46.575 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 619 5.17 %
Rwork0.2256 11359 -
obs0.2271 11978 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.74 Å2 / Biso mean: 39.2059 Å2 / Biso min: 18.98 Å2
Refinement stepCycle: final / Resolution: 2.15→46.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 0 69 1560
Biso mean---45.71 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021522
X-RAY DIFFRACTIONf_angle_d0.6692065
X-RAY DIFFRACTIONf_chiral_restr0.024235
X-RAY DIFFRACTIONf_plane_restr0.003267
X-RAY DIFFRACTIONf_dihedral_angle_d13.106574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1502-2.36650.29941290.26792630275994
2.3665-2.70890.30421690.258128292998100
2.7089-3.41280.28411720.238728533025100
3.4128-46.58580.21711490.202930473196100
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)
11.75030.9996-0.44781.7185-0.06861.4525-0.1349-0.1034-0.09070.27980.1147-0.034-0.2417-0.2173-0.01750.27640.0781-0.00710.1917-0.03260.2396-11.34590.60740.5426
24.71570.086-0.04762.3662-0.55121.89470.0581-0.48280.73380.4212-0.12990.0162-0.91970.29960.15540.5185-0.0448-0.06990.2531-0.02060.3871-2.12549.39772.9812
31.3536-0.48030.66711.1222-0.09481.1803-0.1958-0.22080.13520.22630.20450.1912-0.5307-0.5022-0.0770.38480.1223-0.04250.3744-0.04780.3668-16.94632.82450.1156
41.5845-0.57760.61210.9714-0.16940.2464-0.087-0.95770.62750.5268-0.13740.4322-1.0229-0.34890.06110.60170.29230.07490.5311-0.08370.4504-18.17617.38667.7011
51.39740.7807-1.10561.86530.3041.4817-0.2143-0.04280.09540.36070.29970.3973-0.3249-0.9916-0.06650.32730.1285-0.00360.4683-0.00240.3222-22.6022-4.7939-3.8043
62.9619-0.43870.29112.218-0.58673.825-0.12420.3333-0.2087-0.1660.10250.01660.1491-0.34130.02630.219-0.01080.0010.295-0.04610.2413-13.0794-8.642-12.3408
71.3774-0.2571-0.0851.67650.65531.9832-0.06070.2039-0.4293-0.74520.1507-0.2016-0.48560.0009-0.17820.2742-0.03870.02780.4793-0.07550.2979-10.0759-4.2083-23.3481
81.98071.03630.02513.40430.78121.6143-0.08870.83950.388-0.55910.32190.4013-0.3046-0.0152-0.26370.4130.0419-0.02590.55850.1320.3711-14.164.0783-19.6749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 30 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 57 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 67 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 87 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 88 through 155 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 171 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 172 through 194 )A0

+
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