[English] 日本語
Yorodumi
- PDB-4ixn: Crystal Structure of Zn(II)-bound E37A,C66A,C67A triple mutant Yj... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ixn
TitleCrystal Structure of Zn(II)-bound E37A,C66A,C67A triple mutant YjiA GTPase
ComponentsUncharacterized GTP-binding protein YjiA
KeywordsHYDROLASE / P-loop GTPase / G-protein / metal homeostasis
Function / homology
Function and homology information


transition metal ion binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / DNA damage response / GTP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Hypothetical Protein Yjia; Chain: A;domain 2 / CobW-like, C-terminal domain / : / Cobalamin synthesis protein cobW C-terminal domain / Cobalamin (vitamin B12) biosynthesis CobW-like, C-terminal / CobW-like, C-terminal domain superfamily / Cobalamin synthesis protein cobW C-terminal domain / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases ...Hypothetical Protein Yjia; Chain: A;domain 2 / CobW-like, C-terminal domain / : / Cobalamin synthesis protein cobW C-terminal domain / Cobalamin (vitamin B12) biosynthesis CobW-like, C-terminal / CobW-like, C-terminal domain superfamily / Cobalamin synthesis protein cobW C-terminal domain / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsJost, M. / Drennan, C.L.
CitationJournal: Biochemistry / Year: 2013
Title: Metal binding properties of Escherichia coli YjiA, a member of the metal homeostasis-associated COG0523 family of GTPases.
Authors: Sydor, A.M. / Jost, M. / Ryan, K.S. / Turo, K.E. / Douglas, C.D. / Drennan, C.L. / Zamble, D.B.
History
DepositionJan 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Jul 3, 2013Group: Database references
Revision 1.4Jul 24, 2013Group: Database references
Revision 1.5Jan 1, 2014Group: Database references
Revision 1.6Mar 5, 2014Group: Database references
Revision 1.7Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_conn.ptnr2_label_seq_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: Uncharacterized GTP-binding protein YjiA
B: Uncharacterized GTP-binding protein YjiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5377
Polymers71,1492
Non-polymers3885
Water4,612256
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-105 kcal/mol
Surface area27340 Å2
MethodPISA
2
A: Uncharacterized GTP-binding protein YjiA
hetero molecules

B: Uncharacterized GTP-binding protein YjiA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5377
Polymers71,1492
Non-polymers3885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3210 Å2
ΔGint-98 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.071, 68.436, 77.699
Angle α, β, γ (deg.)90.00, 104.23, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE IS NOT KNOWN CRYSTAL STRUCTURE LIKELY CONTAINS A DIMER, BUT ZN(II)-BOUND PROTEIN OLIGOMERIZES IN SOLUTION, AS INDICATED BY SIZE EXCLUSION CHROMATOGRAPHY. PHYSIOLOGICAL OLIGOMERIZATION STATE UNKNOWN

-
Components

#1: Protein Uncharacterized GTP-binding protein YjiA


Mass: 35574.445 Da / Num. of mol.: 2 / Mutation: E37A, C66A, C67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4352, JW5790, yjiA / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24203
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 uL of 12.4 mg/mL triple mutant YjiA in 0.1 M NaCl, 1 mM TCEP, 25 mM HEPES, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.3 M ammonium sulfate, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING ...Details: 1.5 uL of 12.4 mg/mL triple mutant YjiA in 0.1 M NaCl, 1 mM TCEP, 25 mM HEPES, mixed with 0.3 uL 0.1 M CaCl2 and 1.5 uL 1.3 M ammonium sulfate, 0.1 M HEPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2012
RadiationMonochromator: Si(111) cryo-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→75.3 Å / Num. all: 35715 / Num. obs: 35715 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rsym value: 0.085 / Net I/σ(I): 18.6
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1784 / Rsym value: 0.59 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
APSconsoledata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→75.3 Å / SU ML: 0.24 / Isotropic thermal model: isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1747 4.95 %same as for Zn(II)-soaked WT YjiA between 30 and 2.57 A resolution, random for remainder
Rwork0.2027 ---
obs0.2044 35309 98.31 %-
all-35309 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.79 Å2
Refinement stepCycle: LAST / Resolution: 2.05→75.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 13 256 5080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084986
X-RAY DIFFRACTIONf_angle_d0.7276782
X-RAY DIFFRACTIONf_dihedral_angle_d11.381778
X-RAY DIFFRACTIONf_chiral_restr0.049803
X-RAY DIFFRACTIONf_plane_restr0.003888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11030.29641400.25562790X-RAY DIFFRACTION99
2.1103-2.17850.32481360.24772787X-RAY DIFFRACTION99
2.1785-2.25630.28471460.23852822X-RAY DIFFRACTION99
2.2563-2.34670.26841330.22592779X-RAY DIFFRACTION97
2.3467-2.45350.26041500.23472787X-RAY DIFFRACTION99
2.4535-2.58280.26911450.22192797X-RAY DIFFRACTION99
2.5828-2.74470.24981650.21512768X-RAY DIFFRACTION98
2.7447-2.95660.24911220.22242806X-RAY DIFFRACTION98
2.9566-3.25410.24221360.2092813X-RAY DIFFRACTION99
3.2541-3.7250.20521600.18042775X-RAY DIFFRACTION98
3.725-4.6930.2151600.1652835X-RAY DIFFRACTION99
4.693-75.36510.22141540.19842803X-RAY DIFFRACTION96
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)
12.5477-0.3702-0.03783.683-1.34344.3439-0.0464-0.6708-0.48340.39590.1090.06460.2299-0.4405-0.01340.4002-0.0299-0.03520.50580.11030.324823.20127.848128.0714
22.74740.11760.55542.74920.5663.4048-0.075-0.00850.1904-0.1450.10220.0001-0.0881-0.1563-0.04870.20940.0008-0.01120.14480.030.201823.110722.12756.1208
33.4920.2066-1.14364.36251.60354.166-0.13050.2676-0.1709-0.1890.0378-0.06750.13080.02050.10280.25850.0142-0.02490.2726-0.00820.212950.46676.75789.703
42.08050.49140.19663.20880.97393.6871-0.0488-0.08540.15910.50650.0625-0.120.21570.07510.02090.25420.0167-0.01410.1915-0.01290.178151.069721.335131.5267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resseq 1:123)
2X-RAY DIFFRACTION2(chain 'A' and resseq 124:318)
3X-RAY DIFFRACTION3(chain 'B' and resseq 1:123)
4X-RAY DIFFRACTION4(chain 'B' and resseq 124:318)

+
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://pdbjlc1.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