[English] 日本語
Yorodumi
- PDB-1wl8: Crystal structure of PH1346 protein from Pyrococcus horikoshii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wl8
TitleCrystal structure of PH1346 protein from Pyrococcus horikoshii
ComponentsGMP synthase [glutamine-hydrolyzing] subunit A
KeywordsLIGASE / Transferase / GATases / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / glutamine metabolic process / ATP binding
Similarity search - Function
GMP synthase (glutamine-hydrolyzing) subunit A / GMP synthase, glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / GMP synthase [glutamine-hydrolyzing] subunit A
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of Glutamide Amido Transferase from Pyrococcus horikoshii OT3
Authors: Lokanath, N.K. / Kunishima, N.
History
DepositionJun 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GMP synthase [glutamine-hydrolyzing] subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6403
Polymers21,5441
Non-polymers962
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.808, 63.480, 65.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biologocal assembly is monomer, consists of one polypetide chain in the asymmetric unit

-
Components

#1: Protein GMP synthase [glutamine-hydrolyzing] subunit A / Glutamine amido transferase


Mass: 21544.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O59071, GMP synthase (glutamine-hydrolysing)
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.3 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.8
Details: Acetate, PEG, pH 4.8, microbatch, temperature 295.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 21, 2004 / Details: RH COATED BENT-CYLINDRICAL MIRROR
RadiationMonochromator: Sl111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. all: 33392 / Num. obs: 33220 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 10.81 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.7
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.25 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QDL

1qdl


Resolution: 1.45→28.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.834 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17365 1758 5 %RANDOM
Rwork0.15544 ---
all0.15638 33392 --
obs0.15638 33220 99.83 %-
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: 9.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2---0.21 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 1 215 1720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211541
X-RAY DIFFRACTIONr_bond_other_d0.0030.021422
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9832073
X-RAY DIFFRACTIONr_angle_other_deg0.85633334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375185
X-RAY DIFFRACTIONr_chiral_restr0.0890.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021675
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02290
X-RAY DIFFRACTIONr_nbd_refined0.2780.2319
X-RAY DIFFRACTIONr_nbd_other0.2560.21654
X-RAY DIFFRACTIONr_nbtor_other0.0920.2866
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.217
X-RAY DIFFRACTIONr_mcbond_it0.8151.5930
X-RAY DIFFRACTIONr_mcangle_it1.57121504
X-RAY DIFFRACTIONr_scbond_it2.4573611
X-RAY DIFFRACTIONr_scangle_it4.0324.5569
LS refinement shellResolution: 1.451→1.489 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.192 108
Rwork0.172 2405

+
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