[English] 日本語
Yorodumi
- PDB-3reu: Crystal structure of the archaeal asparagine synthetase A complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3reu
TitleCrystal structure of the archaeal asparagine synthetase A complexed with L-Aspartic acid and Adenosine triphosphate
ComponentsAsnS-like asparaginyl-tRNA synthetase related protein
KeywordsLIGASE / ATP binding / Aspartic acid binding / 7 stranded anti parallel beta-sheet
Function / homology
Function and homology information


asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / ATP binding / metal ion binding
Similarity search - Function
Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / ADENOSINE-5'-TRIPHOSPHATE / AsnS-like asparaginyl-tRNA synthetase related protein
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBlaise, M. / Frechin, M. / Charron, C. / Roy, H. / Sauter, C. / Lorber, B. / Olieric, V. / Kern, D.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of the Archaeal Asparagine Synthetase: Interrelation with Aspartyl-tRNA and Asparaginyl-tRNA Synthetases.
Authors: Blaise, M. / Frechin, M. / Olieric, V. / Charron, C. / Sauter, C. / Lorber, B. / Roy, H. / Kern, D.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Sep 13, 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_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.ptnr3_label_seq_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_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: AsnS-like asparaginyl-tRNA synthetase related protein
B: AsnS-like asparaginyl-tRNA synthetase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,55611
Polymers68,2632
Non-polymers1,2939
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-112 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.470, 61.180, 156.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein AsnS-like asparaginyl-tRNA synthetase related protein


Mass: 34131.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: asnS-like, PYRAB02460, PAB2356 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V228
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100mM TRis pH7, 0.2M NaCl, 32% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 44981 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.34
Reflection shellResolution: 1.9→2 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NNH

1nnh


Resolution: 1.9→48.249 Å / SU ML: 0.23 / σ(F): 2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 1996 4.44 %random
Rwork0.1702 ---
all0.172 44981 --
obs0.172 44979 99.39 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.556 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.118 Å20 Å20 Å2
2--0.3109 Å20 Å2
3---5.7338 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 77 299 5158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074983
X-RAY DIFFRACTIONf_angle_d1.1256737
X-RAY DIFFRACTIONf_dihedral_angle_d13.4111916
X-RAY DIFFRACTIONf_chiral_restr0.078698
X-RAY DIFFRACTIONf_plane_restr0.004858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.3071330.24413051X-RAY DIFFRACTION100
1.9475-2.00020.31891420.21723025X-RAY DIFFRACTION100
2.0002-2.0590.26541400.20183054X-RAY DIFFRACTION100
2.059-2.12550.21991390.17553031X-RAY DIFFRACTION100
2.1255-2.20150.22471400.17613052X-RAY DIFFRACTION100
2.2015-2.28960.22731460.16873050X-RAY DIFFRACTION100
2.2896-2.39380.22021500.18643028X-RAY DIFFRACTION100
2.3938-2.520.2761370.18443072X-RAY DIFFRACTION100
2.52-2.67790.24691420.18613069X-RAY DIFFRACTION100
2.6779-2.88460.2331460.1823078X-RAY DIFFRACTION100
2.8846-3.17490.20271430.1813065X-RAY DIFFRACTION99
3.1749-3.63410.20021460.16083115X-RAY DIFFRACTION99
3.6341-4.57810.16121400.13663083X-RAY DIFFRACTION98
4.5781-48.2640.17151520.15533210X-RAY DIFFRACTION97
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)
10.0012-0.00520.00190.0834-0.01740.0371-0.02110.0330.02120.04670.0381-0.02630.01550.0338-0.00950.04370.0135-0.0540.09490.01820.083221.8095-6.914125.2564
20.0038-0.0058-0.00230.0120.01290.0202-0.0427-0.0125-0.0331-0.0098-0.03410.06450.0105-0.01270.0316-0.0185-0.0213-0.00540.0998-0.02010.166914.69631.00827.6565
30.0087-0.00460.01630.01720.00840.0373-0.03980.0575-0.01270.0081-0.0165-0.00020.04390.04980.02960.00170.05290.00370.1014-0.01950.188528.3864-17.63148.5695
40.00710.01320.00690.030.01930.0249-0.06820.0668-0.0659-0.0001-0.01840.0551-0.02530.00790.0254-0.0823-0.00650.01280.0697-0.01370.075717.9061-5.64453.0005
50.0761-0.0235-0.05590.3587-0.04630.0635-0.0356-0.01060.00760.13530.01840.0589-0.07370.00130.01010.0957-0.0097-0.01770.06730.01190.066518.462810.065919.7825
60.0021-0.00110.00610.0042-0.00880.0406-0.0010.01590.00060.006-0.00620.0133-0.00630.0052-0.0010.06190.01730.06150.073-0.03190.03795.54752.877726.2278
70.0289-0.0235-0.01870.06960.04310.0227-0.009-0.07950.00370.08330.00070.0317-0.01340.03460.00170.19840.0028-0.05790.1245-0.02860.01520.725213.290228.5139
80.02050.00250.01850.0159-0.01160.029-0.01470.0191-0.0024-0.0460.0045-0.00120.02570.06660.00310.2560.00390.01290.1834-0.09720.095124.596226.655336.7207
90.0108-0.00560.0010.00360.00070.0023-0.0456-0.02920.00960.01640.00220.0069-0.0112-0.01380.02870.2562-0.02390.02190.1389-0.07230.042215.630124.12135.8077
100.04890.0198-0.01580.00910.01190.0395-0.0195-0.01840.00050.0204-0.01240.0288-0.0347-0.01340.00780.160.01660.09940.0337-0.0858-0.03489.213414.939538.2646
110.00970.00360.02780.01170.00620.0809-0.00940.0198-0.0055-0.01040.00460.0022-0.0353-0.01920.00110.2426-0.04960.11630.23240.05080.13830.65580.220636.9468
120.00570.00480.00420.00830.01140.02160.0034-0.00240.00230.0211-0.00240.0069-0.0165-0.0010.00090.0728-0.0029-0.0711-0.0184-0.0731-0.048719.168218.792417.023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:32)
2X-RAY DIFFRACTION2chain 'A' and (resseq 33:125)
3X-RAY DIFFRACTION3chain 'A' and (resseq 126:179)
4X-RAY DIFFRACTION4chain 'A' and (resseq 180:294)
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:65)
6X-RAY DIFFRACTION6chain 'B' and (resseq 66:85)
7X-RAY DIFFRACTION7chain 'B' and (resseq 86:148)
8X-RAY DIFFRACTION8chain 'B' and (resseq 149:169)
9X-RAY DIFFRACTION9chain 'B' and (resseq 170:197)
10X-RAY DIFFRACTION10chain 'B' and (resseq 198:239)
11X-RAY DIFFRACTION11chain 'B' and (resseq 240:257)
12X-RAY DIFFRACTION12chain 'B' and (resseq 258:294)

+
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