[English] 日本語
Yorodumi
- PDB-2xti: Asparaginyl-tRNA synthetase from Brugia malayi complexed with ATP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xti
TitleAsparaginyl-tRNA synthetase from Brugia malayi complexed with ATP:Mg and L-Asp-beta-NOH adenylate:PPi:Mg
ComponentsASPARAGINYL-TRNA SYNTHETASE\, CYTOPLASMIC\, PUTATIVE
KeywordsLIGASE / ATP-BINDING / PROTEIN BIOSYNTHESIS / FILARIASIS
Function / homology
Function and homology information


Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-NB8 / PYROPHOSPHATE 2- / :
Similarity search - Component
Biological speciesBRUGIA MALAYI (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCrepin, T. / Haertlein, M. / Kron, M. / Cusack, S.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: A Hybrid Structural Model of the Complete Brugia Malayi Cytoplasmic Asparaginyl-tRNA Synthetase.
Authors: Crepin, T. / Peterson, F. / Haertlein, M. / Jensen, D. / Wang, C. / Cusack, S. / Kron, M.
#1: Journal: J. Comput. Aided Mol. Des. / Year: 2006
Title: Discovering New Classes of Brugia Malayi Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change.
Authors: Sukuru, S.C.K. / Crepin, T. / Milev, Y. / Marsh, L.C. / Hill, J.B. / Anderson, R.J. / Morris, J.C. / Rohatgi, A. / O'Mahony, G. / Grotli, M. / Danel, F. / Page, M.G.P. / Hartlein, M. / ...Authors: Sukuru, S.C.K. / Crepin, T. / Milev, Y. / Marsh, L.C. / Hill, J.B. / Anderson, R.J. / Morris, J.C. / Rohatgi, A. / O'Mahony, G. / Grotli, M. / Danel, F. / Page, M.G.P. / Hartlein, M. / Cusack, S. / Kron, M.A. / Kuhn, L.A.
History
DepositionOct 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 29, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.country / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ASPARAGINYL-TRNA SYNTHETASE\, CYTOPLASMIC\, PUTATIVE
B: ASPARAGINYL-TRNA SYNTHETASE\, CYTOPLASMIC\, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,73911
Polymers100,4332
Non-polymers1,3069
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-86.8 kcal/mol
Surface area34730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.920, 106.390, 161.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein ASPARAGINYL-TRNA SYNTHETASE\, CYTOPLASMIC\, PUTATIVE


Mass: 50216.305 Da / Num. of mol.: 2
Fragment: CATALYTICALLY ACTIVE FRAGMENT LACKING N-TERMINAL EXTENSION, RESIDUES 112-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRUGIA MALAYI (agent of lymphatic filariasis)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8PWE4, leucine-tRNA ligase

-
Non-polymers , 5 types, 255 molecules

#2: Chemical ChemComp-NB8 / 5'-O-[(R)-{[(2S)-2-amino-4-(hydroxyamino)-4-oxobutanoyl]oxy}(hydroxy)phosphoryl]adenosine


Type: L-peptide linking / Mass: 477.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N7O10P
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: ROOM TEMPERATURE HANGING-DROP VAPOUR DIFFUSION IN 0.1 M HEPES PH 8.5, 200MM SODIUM ACETATE USING 17-19 % PEG 4000 AS PRECIPITANT. PROTEIN CONCENTRATION OF 2.5MG/ML WITH 10 MM ATP:MGCL2, 10 MM L-ASP-BETA-NOH.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 38929 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.3 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XGT

2xgt


Resolution: 2.4→48.22 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.861 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.29837 1558 4 %RANDOM
Rwork0.21278 ---
obs0.21606 37371 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.48 Å20 Å20 Å2
2---1.59 Å20 Å2
3----3.89 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6968 0 78 246 7292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227199
X-RAY DIFFRACTIONr_bond_other_d0.0010.024943
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9729757
X-RAY DIFFRACTIONr_angle_other_deg0.863311975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88523.669357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.024151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5741558
X-RAY DIFFRACTIONr_chiral_restr0.0780.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021510
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4931.54299
X-RAY DIFFRACTIONr_mcbond_other0.0981.51738
X-RAY DIFFRACTIONr_mcangle_it0.89426948
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.31832900
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0644.52809
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 110 -
Rwork0.265 2642 -
obs--100 %
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)
12.0461-0.43010.39741.6997-0.35293.8965-0.00470.064-0.09390.13340.037-0.2318-0.17670.6873-0.03240.4659-0.0055-0.01280.2702-0.00260.223828.628-6.6991.458
20.17610.3026-0.34791.9233-0.02172.0666-0.03810.0201-0.0552-0.01250.03130.04540.1618-0.19260.00680.0147-0.0066-0.00280.18310.00140.217111.57-14.08452.363
32.0557-0.3565-0.37232.76420.51336.07920.0515-0.00250.1425-0.3779-0.1385-0.47580.08930.74790.0870.22190.00860.07240.21680.03970.291732.451-1.72124.912
40.23390.1625-0.02031.7396-0.56312.43540.07290.01610.06480.4159-0.0417-0.0177-0.82240.0927-0.03120.4712-0.0349-0.010.1478-0.00450.193117.73813.76463.764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A112 - 204
2X-RAY DIFFRACTION2A205 - 548
3X-RAY DIFFRACTION3B113 - 204
4X-RAY DIFFRACTION4B205 - 548

+
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