[English] 日本語
Yorodumi
- PDB-6g7w: Crystal structure of NHL repeat containing domain of human NHLRC2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g7w
TitleCrystal structure of NHL repeat containing domain of human NHLRC2
ComponentsNHL repeat-containing protein 2
KeywordsUNKNOWN FUNCTION / NHL repeat containing / structural domain / protein binding
Function / homology
Function and homology information


platelet alpha granule lumen / Platelet degranulation / extracellular region / cytosol
Similarity search - Function
NHL2, NHL repeat domain / NHL repeat profile. / Thioredoxin-like / NHL repeat / NHL repeat / Thioredoxin-like fold / Six-bladed beta-propeller, TolB-like / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
NHL repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.746 Å
AuthorsBiterova, E. / Uusimaa, J. / Hinttala, R. / Ruddock, L.W.
Funding support Finland, 4items
OrganizationGrant numberCountry
Academy of Finland266457 Finland
Academy of Finland272573 Finland
Academy of Finland266498 Finland
Academy of Finland303996 Finland
CitationJournal: PLoS ONE / Year: 2018
Title: Structural analysis of human NHLRC2, mutations of which are associated with FINCA disease.
Authors: Biterova, E. / Ignatyev, A. / Uusimaa, J. / Hinttala, R. / Ruddock, L.W.
History
DepositionApr 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NHL repeat-containing protein 2


Theoretical massNumber of molelcules
Total (without water)39,1111
Polymers39,1111
Non-polymers00
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.631, 46.491, 70.302
Angle α, β, γ (deg.)90.000, 102.900, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein NHL repeat-containing protein 2


Mass: 39110.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHLRC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NBF2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Li2SO4, 0.1 M BisTris pH 5.5, 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.42→46.331 Å / Num. obs: 42106 / % possible obs: 67.5 % / Redundancy: 2.917 % / Biso Wilson estimate: 17.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.058 / Χ2: 1.036 / Net I/σ(I): 12.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.42-1.461.5581.0250.452600.3261.4395.7
1.46-1.51.8450.8140.677010.3321.12615.7
1.5-1.541.9080.6030.9210950.5090.83225.3
1.54-1.592.0540.4921.215570.6640.66436.6
1.59-1.642.2130.431.5618480.7370.56845.1
1.64-1.72.460.3442.1222050.8090.44155.9
1.7-1.772.6450.2762.8526400.8970.34669
1.77-1.842.9060.2094.0732480.9440.25688.5
1.84-1.923.1580.1565.9534630.9690.18898.1
1.92-2.013.0950.1197.7433500.980.14498
2.01-2.1230.0999.5830580.9860.12195.8
2.12-2.253.180.08311.8130030.9910.09998.5
2.25-2.413.1550.06914.0628240.9930.08398.4
2.41-2.63.110.06115.7926090.9940.07497.1
2.6-2.853.2830.0519.5924270.9960.0699.1
2.85-3.183.2210.03825.5822100.9980.04598.8
3.18-3.673.1960.02933.1719350.9980.03597.2
3.67-4.53.2080.02438.6116700.9990.02998.9
4.5-6.363.1540.02339.2212820.9990.02797.3
6.36-46.3312.9990.02240.457210.9990.02695.8

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.746→46.331 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.37
RfactorNum. reflection% reflection
Rfree0.1892 1630 5 %
Rwork0.1548 --
obs0.1565 32600 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.88 Å2 / Biso mean: 21.8647 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: final / Resolution: 1.746→46.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 0 320 2971
Biso mean---30.45 -
Num. residues----349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7459-1.79720.27321100.22442081219178
1.7972-1.85520.22831340.20262546268095
1.8552-1.92160.23561370.16172599273699
1.9216-1.99850.22731380.15992630276898
1.9985-2.08940.19331360.15672578271497
2.0894-2.19960.21691370.16282616275397
2.1996-2.33740.22251380.16232619275798
2.3374-2.51790.22791390.16382641278098
2.5179-2.77120.22971390.17322629276898
2.7712-3.17210.20391400.1642662280299
3.1721-3.99620.15511390.14112654279398
3.9962-46.34690.12531430.12392715285897
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)
12.0346-0.8137-0.69692.12030.43133.86210.0320.1366-0.0587-0.10540.0131-0.0070.0520.0934-0.03240.0838-0.0067-0.00570.09670.0060.116824.848628.3134.6399
22.53990.3376-0.61531.4587-0.77372.40680.00090.15750.0656-0.05440.05870.06050.0208-0.1817-0.05170.08570.0039-0.01730.104-0.00220.09718.60727.13029.095
32.8322-0.24640.2380.8355-0.25682.54390.0221-0.1099-0.28240.010.02420.06710.1581-0.171-0.04750.1343-0.02270.01230.11930.00840.14679.023914.700822.2819
41.98150.3499-0.83040.7959-0.4221.24870.0164-0.2314-0.08790.0657-0.075-0.08730.0240.15170.06390.1229-0.0009-0.0260.12360.01280.117329.4621.335222.2983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 220 through 262 )A220 - 262
2X-RAY DIFFRACTION2chain 'A' and (resid 263 through 370 )A263 - 370
3X-RAY DIFFRACTION3chain 'A' and (resid 371 through 451 )A371 - 451
4X-RAY DIFFRACTION4chain 'A' and (resid 452 through 572 )A452 - 572

+
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