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- PDB-6vwp: Crystal structure of E. coli guanosine kinase in complex with ppGpp -

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Basic information

Entry
Database: PDB / ID: 6vwp
TitleCrystal structure of E. coli guanosine kinase in complex with ppGpp
ComponentsInosine-guanosine kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


guanosine kinase activity / inosine kinase / inosine kinase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / guanosine tetraphosphate binding / phosphorylation / ATP binding
Similarity search - Function
Guanosine-inosine kinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / GUANOSINE / : / Guanosine-inosine kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsWang, B. / Grant, R.A. / Laub, M.T.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM082899 United States
CitationJournal: Mol.Cell / Year: 2020
Title: ppGpp Coordinates Nucleotide and Amino-Acid Synthesis in E. coli During Starvation.
Authors: Wang, B. / Grant, R.A. / Laub, M.T.
History
DepositionFeb 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inosine-guanosine kinase
B: Inosine-guanosine kinase
C: Inosine-guanosine kinase
D: Inosine-guanosine kinase
E: Inosine-guanosine kinase
F: Inosine-guanosine kinase
G: Inosine-guanosine kinase
H: Inosine-guanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,27651
Polymers390,2798
Non-polymers9,99643
Water0
1
A: Inosine-guanosine kinase
B: Inosine-guanosine kinase
G: Inosine-guanosine kinase
H: Inosine-guanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,12625
Polymers195,1404
Non-polymers4,98621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Inosine-guanosine kinase
D: Inosine-guanosine kinase
E: Inosine-guanosine kinase
F: Inosine-guanosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,15026
Polymers195,1404
Non-polymers5,01022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)245.949, 245.949, 221.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 15 or resid 35...
21(chain B and (resid 0 through 15 or resid 35...
31(chain C and (resid 0 through 15 or resid 35...
41(chain D and (resid 0 through 15 or resid 35...
51(chain E and (resid 0 through 15 or resid 35...
61(chain F and (resid 0 through 344 or resid 355 through 502 or resid 601))
71(chain G and (resid 0 through 15 or resid 35...
81(chain H and (resid 0 through 15 or resid 35...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 0 through 15 or resid 35...A0 - 15
121(chain A and (resid 0 through 15 or resid 35...A35 - 156
131(chain A and (resid 0 through 15 or resid 35...A163
141(chain A and (resid 0 through 15 or resid 35...A0 - 601
151(chain A and (resid 0 through 15 or resid 35...A0 - 601
161(chain A and (resid 0 through 15 or resid 35...A0 - 601
171(chain A and (resid 0 through 15 or resid 35...A0 - 601
181(chain A and (resid 0 through 15 or resid 35...A0 - 601
191(chain A and (resid 0 through 15 or resid 35...A0 - 601
211(chain B and (resid 0 through 15 or resid 35...B0 - 15
221(chain B and (resid 0 through 15 or resid 35...B35 - 156
231(chain B and (resid 0 through 15 or resid 35...B0 - 601
241(chain B and (resid 0 through 15 or resid 35...B0 - 601
251(chain B and (resid 0 through 15 or resid 35...B0 - 601
261(chain B and (resid 0 through 15 or resid 35...B0 - 601
271(chain B and (resid 0 through 15 or resid 35...B0 - 601
281(chain B and (resid 0 through 15 or resid 35...B0 - 601
291(chain B and (resid 0 through 15 or resid 35...B0 - 601
311(chain C and (resid 0 through 15 or resid 35...C0 - 15
321(chain C and (resid 0 through 15 or resid 35...C35 - 156
331(chain C and (resid 0 through 15 or resid 35...C163 - 322
341(chain C and (resid 0 through 15 or resid 35...C323 - 324
351(chain C and (resid 0 through 15 or resid 35...C0 - 601
361(chain C and (resid 0 through 15 or resid 35...C0 - 601
371(chain C and (resid 0 through 15 or resid 35...C0 - 601
381(chain C and (resid 0 through 15 or resid 35...C0 - 601
411(chain D and (resid 0 through 15 or resid 35...D0 - 15
421(chain D and (resid 0 through 15 or resid 35...D35 - 156
431(chain D and (resid 0 through 15 or resid 35...D0 - 601
441(chain D and (resid 0 through 15 or resid 35...D323 - 324
451(chain D and (resid 0 through 15 or resid 35...D0 - 601
461(chain D and (resid 0 through 15 or resid 35...D0 - 601
471(chain D and (resid 0 through 15 or resid 35...D0 - 601
481(chain D and (resid 0 through 15 or resid 35...D0 - 601
511(chain E and (resid 0 through 15 or resid 35...E0 - 15
521(chain E and (resid 0 through 15 or resid 35...E35 - 156
531(chain E and (resid 0 through 15 or resid 35...E163
541(chain E and (resid 0 through 15 or resid 35...E323 - 324
551(chain E and (resid 0 through 15 or resid 35...E0 - 601
561(chain E and (resid 0 through 15 or resid 35...E0 - 601
571(chain E and (resid 0 through 15 or resid 35...E0 - 601
581(chain E and (resid 0 through 15 or resid 35...E0 - 601
611(chain F and (resid 0 through 344 or resid 355 through 502 or resid 601))F0 - 344
621(chain F and (resid 0 through 344 or resid 355 through 502 or resid 601))F355 - 502
631(chain F and (resid 0 through 344 or resid 355 through 502 or resid 601))F601
711(chain G and (resid 0 through 15 or resid 35...G0 - 15
721(chain G and (resid 0 through 15 or resid 35...G35 - 156
731(chain G and (resid 0 through 15 or resid 35...G163 - 322
741(chain G and (resid 0 through 15 or resid 35...G323 - 324
751(chain G and (resid 0 through 15 or resid 35...G0 - 601
761(chain G and (resid 0 through 15 or resid 35...G0 - 601
771(chain G and (resid 0 through 15 or resid 35...G0 - 601
781(chain G and (resid 0 through 15 or resid 35...G0 - 601
811(chain H and (resid 0 through 15 or resid 35...H0 - 15
821(chain H and (resid 0 through 15 or resid 35...H35 - 156
831(chain H and (resid 0 through 15 or resid 35...H0 - 601
841(chain H and (resid 0 through 15 or resid 35...H323 - 324
851(chain H and (resid 0 through 15 or resid 35...H0 - 601
861(chain H and (resid 0 through 15 or resid 35...H0 - 601
871(chain H and (resid 0 through 15 or resid 35...H0 - 601
881(chain H and (resid 0 through 15 or resid 35...H0 - 601

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Components

#1: Protein
Inosine-guanosine kinase


Mass: 48784.902 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: gsk, b0477, JW0466 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEW6, inosine kinase
#2: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp / Guanosine pentaphosphate


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H13N5O5
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.96 Å3/Da / Density % sol: 75.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium acetate pH 4.8, 3.1M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.42→100 Å / Num. obs: 103948 / % possible obs: 99.8 % / Redundancy: 16.7 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.029 / Rrim(I) all: 0.121 / Χ2: 1.005 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.45-3.5115.31.7551930.6990.4611.810.425100
3.51-3.57141.4350530.7690.3931.4840.43598.7
3.57-3.6414.31.1551320.8220.3131.1930.44499.3
3.64-3.7217.10.95751630.8930.2380.9860.445100
3.72-3.817.80.77151710.9280.1880.7930.465100
3.8-3.8917.90.59951730.9530.1450.6170.502100
3.89-3.98180.48751810.9680.1180.5020.546100
3.98-4.0917.60.37451450.9760.0910.3850.625100
4.09-4.2117.40.31152200.9840.0760.3210.72100
4.21-4.3517.30.25651530.9880.0630.2640.872100
4.35-4.517.10.21652050.990.0540.2231.066100
4.5-4.6816.70.18451800.9920.0460.191.241100
4.68-4.916.30.16751860.9930.0420.1721.362100
4.9-5.1515.40.15552160.9920.040.1611.369100
5.15-5.4814.20.14351510.9930.0390.1481.30998.8
5.48-5.918.30.13252070.9960.0310.1351.259100
5.9-6.4918.40.1152390.9970.0260.1131.461100
6.49-7.4317.90.08652710.9980.0210.0891.708100
7.43-9.3616.60.06453070.9990.0160.0661.987100
9.36-10015.90.04754020.9990.0120.0481.69498.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VWO

6vwo


Resolution: 3.45→49.16 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.63
RfactorNum. reflection% reflection
Rfree0.2423 1991 1.92 %
Rwork0.2 --
obs0.2008 103894 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 392.61 Å2 / Biso mean: 158.6597 Å2 / Biso min: 94.63 Å2
Refinement stepCycle: final / Resolution: 3.45→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26574 0 923 0 27497
Biso mean--166.42 --
Num. residues----3390
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A15791X-RAY DIFFRACTION10.868TORSIONAL
12B15791X-RAY DIFFRACTION10.868TORSIONAL
13C15791X-RAY DIFFRACTION10.868TORSIONAL
14D15791X-RAY DIFFRACTION10.868TORSIONAL
15E15791X-RAY DIFFRACTION10.868TORSIONAL
16F15791X-RAY DIFFRACTION10.868TORSIONAL
17G15791X-RAY DIFFRACTION10.868TORSIONAL
18H15791X-RAY DIFFRACTION10.868TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.42-3.50.37831300.32176772690293
3.5-3.60.32331400.29227192733299
3.6-3.70.31831440.269572027346100
3.7-3.820.3151410.25472917432100
3.82-3.960.28411440.23872907434100
3.96-4.120.29021400.225172997439100
4.12-4.310.27881470.223272757422100
4.31-4.530.25811410.190673207461100
4.53-4.820.22031430.178173017444100
4.82-5.190.2141420.18172817423100
5.19-5.710.22451400.18787334747499
5.71-6.530.24231430.190373377480100
6.53-8.220.20041450.186274327577100
8.23-49.160.22541510.18377577772899

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