[English] 日本語
Yorodumi
- PDB-9j9u: artificial dinuclear Mn-bound metalloprotein 2 (D2:Mn) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j9u
Titleartificial dinuclear Mn-bound metalloprotein 2 (D2:Mn)
ComponentsdTDP-4-dehydrorhamnose 3,5-epimerase
KeywordsISOMERASE / Thermophilic isomerase
Function / homology
Function and homology information


dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose 3,5-epimerase-related / dTDP-4-dehydrorhamnose 3,5-epimerase / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / dTDP-4-dehydrorhamnose 3,5-epimerase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJeong, W.J. / Song, W.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other private2019R1C1C1003863 Korea, Republic Of
CitationJournal: To Be Published
Title: Metal-Installer: A protein designer tool to create metal-binding sites
Authors: Jeong, W.J. / Song, W.J.
History
DepositionAug 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 2.0Jul 23, 2025Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dTDP-4-dehydrorhamnose 3,5-epimerase
B: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0684
Polymers42,9582
Non-polymers1102
Water5,188288
1
A: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules

A: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0684
Polymers42,9582
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3400 Å2
ΔGint-11 kcal/mol
Surface area16470 Å2
MethodPISA
2
B: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules

B: dTDP-4-dehydrorhamnose 3,5-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0684
Polymers42,9582
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area3380 Å2
ΔGint-12 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.481, 52.336, 80.581
Angle α, β, γ (deg.)90.00, 114.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-399-

HOH

21B-353-

HOH

-
Components

#1: Protein dTDP-4-dehydrorhamnose 3,5-epimerase / Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D- ...Thymidine diphospho-4-keto-rhamnose 3 / 5-epimerase / dTDP-4-keto-6-deoxyglucose 3 / dTDP-6-deoxy-D-xylo-4-hexulose 3 / dTDP-L-rhamnose synthase


Mass: 21478.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-d-hexulose 3, 5-epimerase (RmlC)
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: rmlC, MTH_1790 / Production host: Escherichia coli (E. coli)
References: UniProt: O27818, dTDP-4-dehydrorhamnose 3,5-epimerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Li2SO4, 20 % PEG 4000, pH 8.0 0.1M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 38116 / % possible obs: 99.6 % / Redundancy: 6 % / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.049 / Rrim(I) all: 0.123 / Χ2: 1.831 / Net I/σ(I): 7.5 / Num. measured all: 229884
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.84-1.874.50.54119120.7840.9370.2790.6120.67399
1.87-1.914.90.46918750.8630.9630.2320.5250.71699.7
1.91-1.945.20.41418700.8770.9670.1990.4610.86299.2
1.94-1.985.60.36818860.9010.9740.1690.4070.9699.4
1.98-2.036.10.32118840.9390.9840.1410.3521.11699.4
2.03-2.076.40.2918900.960.990.1230.3161.16399.6
2.07-2.126.50.26919060.9590.9890.1130.2921.24499.3
2.12-2.186.40.24618710.9620.990.1050.2681.35699.2
2.18-2.256.40.21418750.9710.9930.0910.2331.51199.4
2.25-2.326.20.20118880.9710.9930.0870.2191.58999.5
2.32-2.46.20.18419250.9770.9940.080.2021.63399.9
2.4-2.55.80.1719090.9770.9940.0770.1871.70699.8
2.5-2.616.30.15419000.9840.9960.0670.1681.88199.9
2.61-2.756.40.13619210.9870.9970.0590.1482.10499.7
2.75-2.925.90.11819220.9860.9960.0530.132.17399.9
2.92-3.156.40.10619050.990.9980.0460.1162.6599.9
3.15-3.466.60.09219160.9930.9980.0390.12.949100
3.46-3.966.50.07919350.9950.9990.0330.0863.186100
3.96-4.996.10.06819310.9960.9990.030.0743.221100
4.99-506.30.06619950.9960.9990.0280.0722.69699.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.551 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24699 1752 5 %RANDOM
Rwork0.19813 ---
obs0.20054 33331 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20.36 Å2
2---0.43 Å20 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.9→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 2 288 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123111
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162798
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.8324216
X-RAY DIFFRACTIONr_angle_other_deg0.5541.7816451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7765366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.354526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35210515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02766
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9212.0361467
X-RAY DIFFRACTIONr_mcbond_other1.9172.0361467
X-RAY DIFFRACTIONr_mcangle_it2.7013.6471832
X-RAY DIFFRACTIONr_mcangle_other2.7023.6471833
X-RAY DIFFRACTIONr_scbond_it3.3482.5471644
X-RAY DIFFRACTIONr_scbond_other3.3472.5471645
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2014.4632385
X-RAY DIFFRACTIONr_long_range_B_refined6.5326.7912679
X-RAY DIFFRACTIONr_long_range_B_other6.44326.3312472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 134 -
Rwork0.232 2436 -
obs--99.27 %

+
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