[English] 日本語
Yorodumi
- PDB-6l4b: Crystal structure of human WT NDRG3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l4b
TitleCrystal structure of human WT NDRG3
ComponentsProtein NDRG3
KeywordsSIGNALING PROTEIN / alpha/beta-hydrolase fold / NDRG3 / Unfolded helix
Function / homology
Function and homology information


negative regulation of cell growth / spermatogenesis / cell differentiation / signal transduction / extracellular exosome / cytoplasm
Similarity search - Function
NDRG / Ndr family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, K.R. / Han, B.W.
CitationJournal: Biomolecules / Year: 2020
Title: Structural and Biophysical Analyses of Human N-Myc Downstream-Regulated Gene 3 (NDRG3) Protein.
Authors: Kim, K.R. / Kim, K.A. / Park, J.S. / Jang, J.Y. / Choi, Y. / Lee, H.H. / Lee, D.C. / Park, K.C. / Yeom, Y.I. / Kim, H.J. / Han, B.W.
History
DepositionOct 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Data collection / Category: pdbx_reflns_twin / Item: _pdbx_reflns_twin.diffrn_id
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein NDRG3
B: Protein NDRG3
E: Protein NDRG3
F: Protein NDRG3
C: Protein NDRG3
D: Protein NDRG3


Theoretical massNumber of molelcules
Total (without water)248,6986
Polymers248,6986
Non-polymers00
Water5,747319
1
A: Protein NDRG3

E: Protein NDRG3


Theoretical massNumber of molelcules
Total (without water)82,8992
Polymers82,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area2010 Å2
ΔGint-11 kcal/mol
Surface area24070 Å2
MethodPISA
2
B: Protein NDRG3
F: Protein NDRG3


Theoretical massNumber of molelcules
Total (without water)82,8992
Polymers82,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area24270 Å2
MethodPISA
3
C: Protein NDRG3

D: Protein NDRG3


Theoretical massNumber of molelcules
Total (without water)82,8992
Polymers82,8992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area1960 Å2
ΔGint-10 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.341, 100.150, 110.744
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Protein NDRG3 / N-myc downstream-regulated gene 3 protein


Mass: 41449.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NDRG3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGV2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 200 mM sodium citrate tribasic dehydrate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.1723
pseudo-merohedral21-h,-k,l20.1769
pseudo-merohedral31-1/2H-3/2K, -1/2H+1/2K, -L30.1945
pseudo-merohedral41-1/2H+3/2K, 1/2H+1/2K, -L40.1289
pseudo-merohedral511/2H+3/2K, 1/2H-1/2K, -L50.1311
pseudo-merohedral611/2H-3/2K, -1/2H-1/2K, -L60.1963
ReflectionResolution: 2.2→50 Å / Num. obs: 95796 / % possible obs: 99.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 15.9
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.641 / Num. unique obs: 4774

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XMQ

2xmq


Resolution: 2.2→46.671 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1848 4347 4.896 %
Rwork0.1677 --
all0.169 --
obs-88790 92.228 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.604 Å2
Baniso -1Baniso -2Baniso -3
1--3.683 Å2-0 Å2-19.234 Å2
2---5.101 Å2-0 Å2
3---8.784 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13134 0 0 319 13453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01313419
X-RAY DIFFRACTIONr_bond_other_d0.0360.01712210
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.63418252
X-RAY DIFFRACTIONr_angle_other_deg2.31.56728476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08451680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68224.386684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.791152208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1011548
X-RAY DIFFRACTIONr_chiral_restr0.040.21770
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215066
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022526
X-RAY DIFFRACTIONr_nbd_refined0.1710.22864
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.211918
X-RAY DIFFRACTIONr_nbtor_refined0.1440.26471
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0620.25270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2498
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0840.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.260.269
X-RAY DIFFRACTIONr_nbd_other0.3060.2249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.220
X-RAY DIFFRACTIONr_mcbond_it0.8283.4576756
X-RAY DIFFRACTIONr_mcbond_other0.8283.4576755
X-RAY DIFFRACTIONr_mcangle_it1.5175.1788424
X-RAY DIFFRACTIONr_mcangle_other1.5165.1798425
X-RAY DIFFRACTIONr_scbond_it0.4273.486662
X-RAY DIFFRACTIONr_scbond_other0.4273.486662
X-RAY DIFFRACTIONr_scangle_it0.8135.2029828
X-RAY DIFFRACTIONr_scangle_other0.8125.2029829
X-RAY DIFFRACTIONr_lrange_it3.16241.32814684
X-RAY DIFFRACTIONr_lrange_other3.15541.33114669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2560.2762330.2394227X-RAY DIFFRACTION62.8435
2.256-2.3180.2642470.2334698X-RAY DIFFRACTION71.5009
2.318-2.3850.3272380.2225013X-RAY DIFFRACTION78.4551
2.385-2.4580.3342430.2415373X-RAY DIFFRACTION86.2805
2.458-2.5380.2592730.235684X-RAY DIFFRACTION94.0926
2.538-2.6270.3612640.235761X-RAY DIFFRACTION98.496
2.627-2.7260.22800.2015530X-RAY DIFFRACTION99.3502
2.726-2.8370.2362470.1875437X-RAY DIFFRACTION100.2469
2.837-2.9630.1583130.1795203X-RAY DIFFRACTION100.0181
2.963-3.1070.2122660.1634942X-RAY DIFFRACTION99.8658
3.107-3.2740.192180.1724742X-RAY DIFFRACTION99.9798
3.274-3.4720.1612520.1594533X-RAY DIFFRACTION100.0418
3.472-3.710.1641830.1384203X-RAY DIFFRACTION100.2973
3.71-4.0060.1122160.1253885X-RAY DIFFRACTION99.3459
4.006-4.3850.1212080.1293595X-RAY DIFFRACTION100.1316
4.385-4.8980.1511740.1213235X-RAY DIFFRACTION100
4.898-5.6470.1411760.152899X-RAY DIFFRACTION99.9025
5.647-6.8940.2181010.1652500X-RAY DIFFRACTION100.077
6.894-9.6580.1951250.1291908X-RAY DIFFRACTION99.7057
9.658-46.6710.134900.1841075X-RAY DIFFRACTION97.653

+
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://pdbjlvh1.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