[English] 日本語
Yorodumi
- PDB-1vj7: Crystal structure of the bifunctional catalytic fragment of RelSe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vj7
TitleCrystal structure of the bifunctional catalytic fragment of RelSeq, the RelA/SpoT homolog from Streptococcus equisimilis.
ComponentsBifunctional RELA/SPOT
KeywordsHYDROLASE / TRANSFERASE / HD domain / alpha beta 2-layer sandwich / helix bundle / manganese / GDP / ppG2':3'p / (P)PPGPP / PPGPP / rela / spot / stringent response / stringent factor / stringent effector / magic spot / rsh
Function / homology
Function and homology information


guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / GTP binding / ATP binding / metal ion binding
Similarity search - Function
RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / Hypothetical protein af1432 / Hypothetical protein af1432 / ACT domain profile. ...RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / Hypothetical protein af1432 / Hypothetical protein af1432 / ACT domain profile. / ACT domain / HD domain profile. / HD domain / TGS domain profile. / TGS / TGS-like / Beta-grasp domain superfamily / Beta Polymerase, domain 2 / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Chem-GPX / : / Bifunctional (p)ppGpp synthase/hydrolase RelA
Similarity search - Component
Biological speciesStreptococcus dysgalactiae subsp. equisimilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR(AS) / Resolution: 2.1 Å
AuthorsHogg, T. / Mechold, U. / Malke, H. / Cashel, M. / Hilgenfeld, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response.
Authors: Hogg, T. / Mechold, U. / Malke, H. / Cashel, M. / Hilgenfeld, R.
History
DepositionFeb 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_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_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: Bifunctional RELA/SPOT
B: Bifunctional RELA/SPOT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7147
Polymers91,2132
Non-polymers1,5015
Water3,531196
1
A: Bifunctional RELA/SPOT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1043
Polymers45,6061
Non-polymers4982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional RELA/SPOT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6104
Polymers45,6061
Non-polymers1,0033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.490, 45.450, 126.470
Angle α, β, γ (deg.)90.00, 109.83, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains two copies of the N-terminal bifunctional catalytic domain. The biological unit is believed to be a single copy of the full-length protein, including the C-terminal ribosome-binding domain.

-
Components

#1: Protein Bifunctional RELA/SPOT / ATP:GTP 3'- pyrophosphotransferase / ppGpp synthetase I / P / ppGpp synthetase / Stringent response- ...ATP:GTP 3'- pyrophosphotransferase / ppGpp synthetase I / P / ppGpp synthetase / Stringent response-like protein


Mass: 45606.352 Da / Num. of mol.: 2
Fragment: (p)ppGpp-3'-pyrophosphohydrolase and (p)ppGpp-synthetase subdomains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus dysgalactiae subsp. equisimilis (bacteria)
Species: Streptococcus dysgalactiae / Strain: subsp. equisimilis / Gene: RELA, REL, SPOT, RSH / Plasmid: PET-21(+)-PENH385 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lambda DE3)
References: UniProt: Q54089, guanosine-3',5'-bis(diphosphate) 3'-diphosphatase, GTP diphosphokinase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GPX / GUANOSINE 5'-DIPHOSPHATE 2':3'-CYCLIC MONOPHOSPHATE


Mass: 505.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O13P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 298 K / pH: 8.5
Details: PEG 8000, sodium chloride, magnesium chloride, TRIS, MES, GDP, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 8.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8445
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1999
RadiationMonochromator: RHODIUM COATED PRE-MIRROR BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR MONOCHROMATOR; SEGMENTED MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8445 Å / Relative weight: 1
ReflectionResolution: 2.1→22.7 Å / Num. obs: 53798 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.1 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
SOLVEphasing
RefinementMethod to determine structure: MAD, MIR(AS) / Resolution: 2.1→22.7 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.327 / SU ML: 0.199 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2700 5 %RANDOM
Rwork0.236 ---
obs0.238 51035 98 %-
all-52098 --
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: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.81 Å20 Å20.12 Å2
2--5.23 Å20 Å2
3----1.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.191 Å0.219 Å
Refinement stepCycle: LAST / Resolution: 2.1→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5139 0 89 196 5424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225325
X-RAY DIFFRACTIONr_bond_other_d0.0010.024858
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9727201
X-RAY DIFFRACTIONr_angle_other_deg0.972311265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.193627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52315992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025739
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021081
X-RAY DIFFRACTIONr_nbd_refined0.2490.31298
X-RAY DIFFRACTIONr_nbd_other0.2180.34915
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0560.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5272
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1630.54
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.350
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.57
X-RAY DIFFRACTIONr_symmetry_hbond_other0.040.51
X-RAY DIFFRACTIONr_mcbond_it1.60923155
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49235093
X-RAY DIFFRACTIONr_scbond_it3.4473.52170
X-RAY DIFFRACTIONr_scangle_it5.1334.52108
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 184
Rwork0.305 3691
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)
15.56250.43880.56861.41490.53822.93950.2572-0.5093-0.04180.1058-0.2572-0.10770.0543-0.280300.176-0.1105-0.02990.1457-0.00720.1529107.0236-12.600578.3517
27.2981.49241.61972.41370.42363.54320.233-0.1647-0.810.0373-0.0991-0.24350.20580.0144-0.13390.1706-0.0773-0.04840.04150.00540.2248124.5004-15.291174.1616
32.77690.7707-0.30511.0143-0.72592.81470.16340.05720.18040.0829-0.0961-0.087-0.1736-0.0489-0.06730.16250.01510.0030.1018-0.03640.2268137.46662.10362.6234
46.48620.9768-0.77711.93841.00616.05530.0354-0.30980.53870.12090.10470.07-0.41830.7931-0.14010.2915-0.15970.01290.2759-0.0450.2101172.733411.487998.5696
58.76381.12152.0912.39131.53996.3961-0.0162-0.4729-0.45960.21260.15360.0130.35370.0178-0.13740.2941-0.07210.04730.14320.01760.2239158.61151.0684101.9017
64.0749-1.7274-2.55130.98941.4952.44530.15230.34670.078-0.20940.05380.1186-0.2935-0.3231-0.20610.4772-0.04670.0350.35680.07740.3093136.119512.586105.6819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 109
2X-RAY DIFFRACTION1A124 - 131
3X-RAY DIFFRACTION1A997
4X-RAY DIFFRACTION1A2002 - 2241
5X-RAY DIFFRACTION2A132 - 152
6X-RAY DIFFRACTION2A159 - 195
7X-RAY DIFFRACTION2A363 - 371
8X-RAY DIFFRACTION3A196 - 341
9X-RAY DIFFRACTION3A998
10X-RAY DIFFRACTION3A2242
11X-RAY DIFFRACTION4B5 - 112
12X-RAY DIFFRACTION4B1997
13X-RAY DIFFRACTION4B1999
14X-RAY DIFFRACTION4B2001 - 2243
15X-RAY DIFFRACTION5B132 - 195
16X-RAY DIFFRACTION5B364 - 370
17X-RAY DIFFRACTION6B196 - 210
18X-RAY DIFFRACTION6B217 - 253
19X-RAY DIFFRACTION6B262 - 340
20X-RAY DIFFRACTION6B1998

+
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