[English] 日本語
Yorodumi
- PDB-2rd5: Structural basis for the regulation of N-acetylglutamate kinase b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rd5
TitleStructural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis thaliana
Components
  • Acetylglutamate kinase-like protein
  • PII protein
KeywordsPROTEIN BINDING / protein-protein complex / regulation of arginine biosynthesis / nitrogen metabolism / Kinase / Transferase / Transcription / Transcription regulation
Function / homology
Function and homology information


acetylglutamate kinase regulator activity / regulation of arginine biosynthetic process via ornithine / anthocyanin-containing compound biosynthetic process / acetylglutamate kinase / acetylglutamate kinase activity / chloroplast thylakoid / response to sucrose / arginine biosynthetic process via ornithine / regulation of fatty acid biosynthetic process / regulation of nitrogen utilization ...acetylglutamate kinase regulator activity / regulation of arginine biosynthetic process via ornithine / anthocyanin-containing compound biosynthetic process / acetylglutamate kinase / acetylglutamate kinase activity / chloroplast thylakoid / response to sucrose / arginine biosynthetic process via ornithine / regulation of fatty acid biosynthetic process / regulation of nitrogen utilization / arginine binding / : / plastid / chloroplast stroma / response to light stimulus / chloroplast / phosphorylation / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein PII / P-II protein family profile. ...N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein PII / P-II protein family profile. / Carbamate kinase / Acetylglutamate kinase-like / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ARGININE / ADENOSINE-5'-TRIPHOSPHATE / N-ACETYL-L-GLUTAMATE / Acetylglutamate kinase, chloroplastic / Nitrogen regulatory protein P-II homolog
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsMizuno, Y. / Moorhead, G.B.G. / Ng, K.K.S.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural Basis for the Regulation of N-Acetylglutamate Kinase by PII in Arabidopsis thaliana.
Authors: Mizuno, Y. / Moorhead, G.B. / Ng, K.K.
History
DepositionSep 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Acetylglutamate kinase-like protein
B: Acetylglutamate kinase-like protein
C: PII protein
D: PII protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,73915
Polymers92,0684
Non-polymers2,67011
Water1,15364
1
A: Acetylglutamate kinase-like protein
B: Acetylglutamate kinase-like protein
C: PII protein
D: PII protein
hetero molecules

A: Acetylglutamate kinase-like protein
B: Acetylglutamate kinase-like protein
C: PII protein
D: PII protein
hetero molecules

A: Acetylglutamate kinase-like protein
B: Acetylglutamate kinase-like protein
C: PII protein
D: PII protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,21645
Polymers276,20512
Non-polymers8,01133
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPISA
Unit cell
Length a, b, c (Å)171.133, 171.133, 171.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11D-1003-

HOH

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Acetylglutamate kinase-like protein


Mass: 31254.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: T8H10.160 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami pLysRARE / References: UniProt: Q9SCL7, acetylglutamate kinase
#2: Protein PII protein / P II nitrogen sensing protein GLB I / At4g01900


Mass: 14779.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g01900, T7B11.16 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami pLysRARE / References: UniProt: Q9ZST4

-
Non-polymers , 6 types, 75 molecules

#3: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-NLG / N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO5
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 4.54 Å3/Da / Density % sol: 72.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8.5% PEG 8000, 8.5% PEG 1000, 0.1 M Na-HEPES, 0.4 M TMAO, 50 mM L-aginine, 2 mM DTT, 12% (w/v) glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.3361 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2007 / Details: vertically focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3361 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 57349 / Num. obs: 57349 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 17.7 % / Biso Wilson estimate: 61.9 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 38
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5692 / Rsym value: 0.95 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxDCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2BUF, 2O66

2buf

2o66


Resolution: 2.51→40 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.315 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.239 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22928 2907 5.1 %RANDOM
Rwork0.20116 ---
all0.20261 54380 --
obs0.20261 54380 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.497 Å2
Refinement stepCycle: LAST / Resolution: 2.51→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6095 0 169 64 6328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226348
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2912.0138572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4415811
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95524.052232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.505151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7131546
X-RAY DIFFRACTIONr_chiral_restr0.080.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024560
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.22527
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.24328
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2185
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.2144
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.80224158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6682.56491
X-RAY DIFFRACTIONr_scbond_it4.23.52445
X-RAY DIFFRACTIONr_scangle_it5.7594.52081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.572 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 221 -
Rwork0.262 3987 -
obs-4206 99.93 %
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)
10.8031-0.2990.06181.87850.00240.4131-0.0130.25990.0368-0.31760.02760.0449-0.02740.0224-0.0146-0.04410.0903-0.0378-0.039-0.0915-0.130886.650748.250545.387
21.0816-0.3490.18431.8145-0.33420.9519-0.01770.11830.0083-0.02160.0182-0.18120.06250.175-0.0005-0.1331-0.03-0.0693-0.11240.0985-0.168779.710693.325148.3085
32.0039-0.44020.6741.1982-0.43012.0778-0.00540.04890.29610.00140.004-0.2775-0.12850.32840.0014-0.1439-0.0923-0.0442-0.1059-0.0105-0.078395.649992.183180.7885
42.5274-0.26270.80881.4496-0.2851.75850.00950.415-0.0705-0.27930.00220.07270.25660.0343-0.0117-0.0064-0.0583-0.1055-0.0217-0.1294-0.119151.840845.307136.2927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 29618 - 297
2X-RAY DIFFRACTION2BB15 - 29616 - 297
3X-RAY DIFFRACTION3CC5 - 1296 - 130
4X-RAY DIFFRACTION4DD5 - 1306 - 131

+
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