[English] 日本語
Yorodumi
- PDB-2hms: Rectangular-shaped octameric ring structure of an RCK domain with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hms
TitleRectangular-shaped octameric ring structure of an RCK domain with NADH bound
ComponentsYuaA protein
KeywordsMEMBRANE PROTEIN / RCK / KTN / KTR / KTRA / KTRAB / ion transporter / symporter
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
: / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...: / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Ktr system potassium uptake protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAlbright, R.A. / Morais-Cabral, J.H.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2006
Title: The RCK Domain of the KtrAB K(+) Transporter: Multiple Conformations of an Octameric Ring.
Authors: Albright, R.A. / Ibar, J.L. / Kim, C.U. / Gruner, S.M. / Morais-Cabral, J.H.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2002
Title: A Mechanism of Regulating Transmembrane Potassium Flux through a Ligand-Mediated Conformational Switch
Authors: Roosild, T.P. / Miller, S. / Booth, I.R. / Choe, S.
#2: Journal: Nature / Year: 2002
Title: Crystal structure and mechanism of a calcium-gated potassium channel
Authors: Jiang, Y. / Lee, A. / Chen, J. / Cadene, M. / Chait, B.T. / MacKinnon, R.
History
DepositionJul 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 7 .. 144 C 7 .. 144 0.245 M 1 B 7 .. 140 D 7 .. 140 0.146 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK:

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YuaA protein
B: YuaA protein
C: YuaA protein
D: YuaA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9688
Polymers64,3064
Non-polymers2,6624
Water48627
1
A: YuaA protein
B: YuaA protein
C: YuaA protein
D: YuaA protein
hetero molecules

A: YuaA protein
B: YuaA protein
C: YuaA protein
D: YuaA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,93516
Polymers128,6128
Non-polymers5,3248
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_755-x+y+2,y,-z+1/31
Unit cell
Length a, b, c (Å)164.881, 164.881, 57.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, -0.0112, 0.0031), (0.0108, -0.7932, 0.6089), (-0.0044, 0.6089, 0.7932)
Vector: 174.4428, -1.514, 0.7045)
DetailsThe biological assembly is an octameric ring generated from the two dimers of the asymmetric unit by applying these symmetry operators: X, Y, Z and 2+Y-X, Y, 1/3-Z

-
Components

#1: Protein
YuaA protein


Mass: 16076.447 Da / Num. of mol.: 4 / Fragment: RCK core domain (KTN), residues 1-144 / Mutation: C22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yuaA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32080
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 100mM sodium acetate pH 5.2, 2M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 24595 / Num. obs: 24578 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.097 / Χ2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.961 / Num. unique all: 2428 / Χ2: 1.037 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: single domain from PDB entry 1LSU

1lsu


Resolution: 2.7→50 Å / FOM work R set: 0.851 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2322 9.5 %RANDOM
Rwork0.214 ---
obs0.212 23550 96.4 %-
all-24595 --
Solvent computationBsol: 51.66 Å2
Displacement parametersBiso mean: 66.616 Å2
Baniso -1Baniso -2Baniso -3
1-7.916 Å2-5.591 Å20 Å2
2--7.916 Å20 Å2
3----15.832 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4250 0 176 27 4453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 46

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.7-2.720.545430.373442485
2.72-2.740.384380.356436474
2.74-2.760.435460.349401447
2.76-2.780.444350.321438473
2.78-2.810.384460.351443489
2.81-2.830.362460.312437483
2.83-2.850.314570.285433490
2.85-2.880.335310.325448479
2.88-2.90.325500.292430480
2.9-2.930.338580.354429487
2.93-2.960.283490.326438487
2.96-2.990.305470.31448495
2.99-3.020.373500.293469519
3.02-3.050.368540.271445499
3.05-3.080.282560.294431487
3.08-3.110.284370.258473510
3.11-3.150.24510.253453504
3.15-3.190.387580.295483541
3.19-3.220.272560.255422478
3.22-3.270.244550.251448503
3.27-3.310.22590.245485544
3.31-3.350.266700.234451521
3.35-3.40.275430.23475518
3.4-3.450.293600.243450510
3.45-3.510.271630.211461524
3.51-3.560.197540.197467521
3.56-3.630.237490.228472521
3.63-3.690.306440.203470514
3.69-3.760.243410.236491532
3.76-3.840.217420.197492534
3.84-3.920.196490.215457506
3.92-4.010.205460.19483529
4.01-4.110.196480.163486534
4.11-4.220.211470.186464511
4.22-4.350.173410.138496537
4.35-4.490.193570.151465522
4.49-4.650.224490.18484533
4.65-4.840.242510.178485536
4.84-5.060.274530.189463516
5.06-5.320.193690.18476545
5.32-5.660.28410.241489530
5.66-6.090.326510.235479530
6.09-6.70.198610.236479540
6.7-7.670.225620.149477539
7.67-9.650.2570.166490547
9.65-500.275520.228494546
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3nadh_ADJUSTED.param

+
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