[English] 日本語
Yorodumi
- PDB-3b1q: Structure of Burkholderia thailandensis nucleoside kinase (BthNK)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b1q
TitleStructure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with inosine
ComponentsRibokinase, putative
KeywordsTRANSFERASE / Rossmann Fold / kinase / ATP binding / Mg binding / Nucleoside binding
Function / homology
Function and homology information


phosphotransferase activity, alcohol group as acceptor / kinase activity / phosphorylation / nucleotide binding
Similarity search - Function
pfkB family of carbohydrate kinases signature 1. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / INOSINE / Ribokinase, putative
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYasutake, Y. / Ota, H. / Hino, E. / Sakasegawa, S. / Tamura, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity
Authors: Yasutake, Y. / Ota, H. / Hino, E. / Sakasegawa, S. / Tamura, T.
History
DepositionJul 5, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribokinase, putative
B: Ribokinase, putative
C: Ribokinase, putative
D: Ribokinase, putative
E: Ribokinase, putative
F: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,36649
Polymers214,5096
Non-polymers4,85743
Water18,8981049
1
A: Ribokinase, putative
F: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,83516
Polymers71,5032
Non-polymers1,33214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-71 kcal/mol
Surface area23980 Å2
MethodPISA
2
B: Ribokinase, putative
D: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,90212
Polymers71,5032
Non-polymers1,39910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-57 kcal/mol
Surface area24860 Å2
MethodPISA
3
C: Ribokinase, putative
E: Ribokinase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,62921
Polymers71,5032
Non-polymers2,12619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-90 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.110, 85.897, 86.872
Angle α, β, γ (deg.)66.33, 68.47, 67.81
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Ribokinase, putative / / Nucleoside kinase


Mass: 35751.480 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I1158 / Plasmid: pTip-QC2 / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L88 / References: UniProt: Q2SZE4, EC: 2.7.1.143

-
Non-polymers , 5 types, 1092 molecules

#2: Chemical
ChemComp-NOS / INOSINE / Inosine


Mass: 268.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H12N4O5
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL, PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1049 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4
Details: 0.1M Na acetate, 0.2M Ca acetate, 26% PEG 400, pH 4.0, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 21, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 208756 / % possible obs: 97.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 19.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.8 / % possible all: 94

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B1N

3b1n


Resolution: 1.7→47.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.774 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20667 10501 5 %RANDOM
Rwork0.17578 ---
obs0.17733 198251 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.609 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20.96 Å20.16 Å2
2---0.57 Å20.3 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13886 0 314 1049 15249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02114533
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.841.97119646
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08751835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24823.199669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69152270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.09215126
X-RAY DIFFRACTIONr_chiral_restr0.1330.22136
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02111183
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.071.59056
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8214374
X-RAY DIFFRACTIONr_scbond_it2.91235477
X-RAY DIFFRACTIONr_scangle_it4.4964.55259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.704→1.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 727 -
Rwork0.261 13694 -
obs--100 %
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)
11.9242-0.30130.10151.0069-0.6041.09640.0335-0.0276-0.2214-0.042-0.0133-0.01790.09680.0385-0.02020.01170.0065-0.00130.00670.00880.038930.018222.593973.8551
21.4232-0.0386-0.89631.41470.01141.3028-0.01820.10560.0898-0.15550.03620.00070.0641-0.0204-0.0180.08180.0089-0.00430.03370.01460.010336.941243.99827.4592
31.0095-0.46790.36462.24790.28311.26210.0067-0.10480.04650.0411-0.04640.0594-0.0354-0.05160.03970.020.0040.00490.0229-0.00360.008958.113842.3729-13.9499
40.5448-0.45140.25782.0675-0.14351.1219-0.01740.07920.0527-0.2110.00860.03150.00110.04190.00880.0872-0.0133-0.03620.05740.0080.0415-4.802854.678729.2882
51.58140.2398-0.03210.4857-0.59891.3160.0171-0.02410.03980.07460.01970.1295-0.1032-0.1651-0.03680.01350.0080.01990.0392-0.02410.067144.07845.4758-4.3
61.0639-0.2924-0.93981.33320.52731.1186-0.0296-0.0182-0.15950.0833-0.02390.01460.05950.00580.05360.04470.0144-0.01110.0652-0.03290.105819.883310.599533.8854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 311
2X-RAY DIFFRACTION2B2 - 313
3X-RAY DIFFRACTION3C2 - 313
4X-RAY DIFFRACTION4D2 - 316
5X-RAY DIFFRACTION5E2 - 313
6X-RAY DIFFRACTION6F2 - 311

+
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