[English] 日本語
Yorodumi
- PDB-8gr3: Crystal structure of K151L/Y158F mutant of GATase subunit of Meth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gr3
TitleCrystal structure of K151L/Y158F mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase
ComponentsGMP synthase [glutamine-hydrolyzing] subunit A
KeywordsTRANSFERASE / amidotransferase / succinimide / deamidation / thermostability
Function / homology
Function and homology information


GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / ATP binding
Similarity search - Function
GMP synthase (glutamine-hydrolyzing) subunit A / GMP synthase, glutamine amidotransferase / Glutamine amidotransferase / Glutamine amidotransferase class-I / 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
GMP synthase [glutamine-hydrolyzing] subunit A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChandrashekarmath, A. / Bellur, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Science and Engineering Research Board (SERB) India
CitationJournal: To Be Published
Title: Crystal structure of K151L/Y158F mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase
Authors: Chandrashekarmath, A. / Bellur, A. / Balaram, H.
History
DepositionAug 31, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,65310
Polymers84,0774
Non-polymers5766
Water5,134285
1
A: GMP synthase [glutamine-hydrolyzing] subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1152
Polymers21,0191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GMP synthase [glutamine-hydrolyzing] subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1152
Polymers21,0191
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GMP synthase [glutamine-hydrolyzing] subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2113
Polymers21,0191
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GMP synthase [glutamine-hydrolyzing] subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2113
Polymers21,0191
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.410, 93.410, 118.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 188 / Label seq-ID: 1 - 188

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.002183, 0.999998, -0.0002), (0.999998, 0.002183, -0.00035), (-0.00035, -0.000201, -1)-46.77455, 46.61657, -34.96927
3given(-0.912881, 0.407281, 0.027738), (-0.407549, -0.905356, -0.119305), (-0.023478, -0.120215, 0.99247)-61.60341, 23.32529, 12.78455
4given(0.404654, -0.914029, -0.028396), (-0.906258, -0.404979, 0.121194), (-0.122275, -0.023307, -0.992223)-0.98964, 4.29407, -26.47744
5given(-0.40729, -0.905487, -0.119203), (-0.913018, 0.406917, 0.028568), (0.022638, 0.12047, -0.992459)-23.36612, -14.89332, -47.79893
6given(-0.906332, -0.404879, 0.120977), (0.404497, -0.914086, -0.028813), (0.122249, 0.022821, 0.992237)-42.42982, 45.70246, -8.49807
7given(-0.000491, 1, -0.000535), (1, 0.00049, -0.00014), (-0.00014, -0.000535, -1)-46.72974, 46.69407, -34.97034

-
Components

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


Mass: 21019.229 Da / Num. of mol.: 4 / Mutation: K151L,Y158F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: guaAA, MJ1575 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q58970, GMP synthase (glutamine-hydrolysing)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 0.1M MES pH 6.5, 0.2M Ammonium sulfate, 30% PEG monomethyl ether 5000

-
Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.4→59.13 Å / Num. obs: 39690 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.974 / Rmerge(I) obs: 0.26 / Net I/σ(I): 8.8
Reflection shellResolution: 2.4→2.53 Å / Num. unique obs: 5761 / CC1/2: 0.619

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D40

7d40


Resolution: 2.4→57.73 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24129 1944 4.9 %RANDOM
Rwork0.20687 ---
obs0.20858 37711 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.038 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.4→57.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5749 0 30 285 6064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135908
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175446
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.638004
X-RAY DIFFRACTIONr_angle_other_deg2.5881.56812657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00124.727256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00715987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7851513
X-RAY DIFFRACTIONr_chiral_restr0.090.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026552
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021114
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_it0.9020.7163004
X-RAY DIFFRACTIONr_mcbond_other0.9010.7163003
X-RAY DIFFRACTIONr_mcangle_it1.5341.073748
X-RAY DIFFRACTIONr_mcangle_other1.5341.0713749
X-RAY DIFFRACTIONr_scbond_it1.9050.8062904
X-RAY DIFFRACTIONr_scbond_other1.8840.7822881
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7381.1314221
X-RAY DIFFRACTIONr_long_range_B_refined4.1158.4466454
X-RAY DIFFRACTIONr_long_range_B_other4.0448.3756410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.87

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A14391.77
22A14152.95
33B14243.36
44B14082.64
55C14213.22
66D14061.59
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 133 -
Rwork0.265 2794 -
obs--100 %

+
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