[English] 日本語
Yorodumi
- PDB-3ncp: GlnK2 from Archaeoglobus fulgidus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ncp
TitleGlnK2 from Archaeoglobus fulgidus
ComponentsNitrogen regulatory protein P-II (GlnB-2)
KeywordsSIGNALING PROTEIN / PII signaling proteins / nucleotide binding / GlnK / GlnB
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / ATP binding / cytosol
Similarity search - Function
Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits ...Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / P-II protein family profile. / Nitrogen regulatory protein PII / Nitrogen regulatory protein P-II / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nitrogen regulatory protein GlnK2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHelfmann, S. / Lue, W. / Litz, C. / Andrade, S.L.A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Cooperative binding of MgATP and MgADP in the trimeric P(II) protein GlnK2 from Archaeoglobus fulgidus.
Authors: Helfmann, S. / Lu, W. / Litz, C. / Andrade, S.L.
History
DepositionJun 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrogen regulatory protein P-II (GlnB-2)
B: Nitrogen regulatory protein P-II (GlnB-2)
C: Nitrogen regulatory protein P-II (GlnB-2)
D: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2887
Polymers53,1814
Non-polymers1063
Water3,081171
1
A: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9926
Polymers39,8863
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area8010 Å2
ΔGint-88 kcal/mol
Surface area15410 Å2
MethodPISA
2
B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9926
Polymers39,8863
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6760 Å2
ΔGint-48 kcal/mol
Surface area13640 Å2
MethodPISA
3
C: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9926
Polymers39,8863
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area7000 Å2
ΔGint-45 kcal/mol
Surface area12580 Å2
MethodPISA
4
D: Nitrogen regulatory protein P-II (GlnB-2)

D: Nitrogen regulatory protein P-II (GlnB-2)

D: Nitrogen regulatory protein P-II (GlnB-2)


Theoretical massNumber of molelcules
Total (without water)39,8863
Polymers39,8863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area6610 Å2
ΔGint-26 kcal/mol
Surface area12460 Å2
MethodPISA
5
A: Nitrogen regulatory protein P-II (GlnB-2)
B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-2)
B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

A: Nitrogen regulatory protein P-II (GlnB-2)
B: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,98512
Polymers79,7726
Non-polymers2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area17830 Å2
ΔGint-150 kcal/mol
Surface area25990 Å2
MethodPISA
6
C: Nitrogen regulatory protein P-II (GlnB-2)
D: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-2)
D: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules

C: Nitrogen regulatory protein P-II (GlnB-2)
D: Nitrogen regulatory protein P-II (GlnB-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8789
Polymers79,7726
Non-polymers1063
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area15580 Å2
ΔGint-86 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.000, 91.000, 64.432
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11B-120-

CL

21C-120-

CL

31B-128-

HOH

-
Components

#1: Protein
Nitrogen regulatory protein P-II (GlnB-2)


Mass: 13295.301 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_1747, glnK2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O28527
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 4000, Na Acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→45.5 Å / Num. all: 24946 / Num. obs: 24887 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.45 % / Biso Wilson estimate: 46.61 Å2 / Rmerge(I) obs: 0.0612 / Rsym value: 0.0612 / Net I/σ(I): 6.38
Reflection shellResolution: 2.35→2.44 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.3662 / Mean I/σ(I) obs: 2.91 / Num. unique all: 2712 / Rsym value: 0.3662 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
BUSTER2.9.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GNK

2gnk


Resolution: 2.35→37.17 Å / Cor.coef. Fo:Fc: 0.9375 / Cor.coef. Fo:Fc free: 0.9326 / SU R Cruickshank DPI: 0.252 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1225 4.92 %RANDOM
Rwork0.2008 ---
obs0.2018 24875 99.88 %-
all-24887 --
Displacement parametersBiso mean: 43.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.3256 Å20 Å20 Å2
2--0.3256 Å20 Å2
3----0.6512 Å2
Refine analyzeLuzzati coordinate error obs: 0.259 Å
Refinement stepCycle: LAST / Resolution: 2.35→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 3 171 3314
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0131722
X-RAY DIFFRACTIONt_angle_deg1.3642622
X-RAY DIFFRACTIONt_dihedral_angle_d11632
X-RAY DIFFRACTIONt_trig_c_planes872
X-RAY DIFFRACTIONt_gen_planes4495
X-RAY DIFFRACTIONt_it317220
X-RAY DIFFRACTIONt_nbd85
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion20.6
X-RAY DIFFRACTIONt_chiral_improper_torsion4265
X-RAY DIFFRACTIONt_ideal_dist_contact37604
LS refinement shellResolution: 2.35→2.45 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2096 153 4.97 %
Rwork0.1643 2926 -
all0.1666 3079 -
obs--99.88 %

+
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