[English] 日本語
Yorodumi
- PDB-4o8k: Crystal structure of Type III pantothenate kinase from Burkholder... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o8k
TitleCrystal structure of Type III pantothenate kinase from Burkholderia thailandensis, apo structure
ComponentsType III pantothenate kinase
KeywordsTRANSFERASE / SSGCID / Type III pantothenate kinase / Pantothenate / kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Type III pantothenate kinase / Type III pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Type III pantothenate kinase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis, apo structure
Authors: Seattle Structural Genomics Center for Infectious Disease / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionDec 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type III pantothenate kinase
B: Type III pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,71410
Polymers59,2112
Non-polymers5038
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-23 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.940, 95.940, 109.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-560-

HOH

21B-409-

HOH

31B-444-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 3 - 258 / Label seq-ID: 24 - 279

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Type III pantothenate kinase / PanK-III / Pantothenic acid kinase


Mass: 29605.643 Da / Num. of mol.: 2 / Fragment: ButhA.17924.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I0369, coaX / Plasmid: ButhA.17294.a.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T1M2, pantothenate kinase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.15 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents, JCSG+ c5: 800mM KH2PO4, 800mm Na2HPO4, 100mM HEPES/NaOH pH 7.5; ButhA.17924.a.A1.PD0391 at 20.0mg/ml, tray 251248c5, puck iyg6-15, cryo: 25% EG in two steps, VAPOR ...Details: Rigaku Reagents, JCSG+ c5: 800mM KH2PO4, 800mm Na2HPO4, 100mM HEPES/NaOH pH 7.5; ButhA.17924.a.A1.PD0391 at 20.0mg/ml, tray 251248c5, puck iyg6-15, cryo: 25% EG in two steps, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2013
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 56674 / Num. obs: 56269 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 24.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.740.3764.67254744056197.8
1.74-1.790.3116.082901340031100
1.79-1.840.2557.42282623905199.9
1.84-1.90.2218.74275693791199.8
1.9-1.960.15212.8265663697199.8
1.96-2.030.12714.88255163536199.6
2.03-2.110.10417.87248443472199.8
2.11-2.190.08720.81236063301199.7
2.19-2.290.07924228943202199.5
2.29-2.40.06626.92219203041199.7
2.4-2.530.05530.96210242921199.5
2.53-2.690.04834.13199842764199.5
2.69-2.870.04437.87187462588199.4
2.87-3.10.03743.33175572435199.5
3.1-3.40.03349.48159782241199.1
3.4-3.80.03252.05143692036198.8
3.8-4.390.02955.28125471812198.6
4.39-5.380.02657.49107861540198.2
5.38-7.60.02656.1985821215197.1
7.6-500.02357.724551713193.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4O5F, pantothenate-bound structure, residues 85-150

4o5f


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.411 / SU ML: 0.058 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 2797 5 %RANDOM
Rwork0.1619 ---
all0.1631 56674 --
obs0.1631 56234 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.26 Å2 / Biso mean: 29.2943 Å2 / Biso min: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 30 400 4065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193798
X-RAY DIFFRACTIONr_bond_other_d0.0060.023635
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9475204
X-RAY DIFFRACTIONr_angle_other_deg1.20138296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37522.158139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61415501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2561529
X-RAY DIFFRACTIONr_chiral_restr0.0920.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214362
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02873
X-RAY DIFFRACTIONr_mcbond_it1.3931.6612017
X-RAY DIFFRACTIONr_mcbond_other1.3761.662016
X-RAY DIFFRACTIONr_mcangle_it2.1672.4812520
Refine LS restraints NCS

Ens-ID: 1 / Number: 12505 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 173 -
Rwork0.199 3876 -
all-4049 -
obs-4056 97.85 %
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)
12.51761.0733-1.3873.1973-0.7092.9245-0.1619-0.0937-0.2308-0.1704-0.0769-0.24840.77060.47740.23880.23470.13030.05390.10130.0240.126723.45541.25718.6
20.14880.03280.20850.1420.00570.32820.00260.0054-0.03980.00010.0161-0.02980.01450.0076-0.01870.07790.00310.00260.08280.01880.109422.72549.05737.584
31.0369-0.3906-0.04224.2393-4.15174.24830.1616-0.02430.27020.7374-0.0926-0.0595-0.83910.0972-0.0690.4471-0.02650.0670.0264-0.02980.129143.55677.94371.426
40.71840.24660.84730.22680.20581.561-0.0338-0.05570.09260.02370.01240.0468-0.1225-0.02840.02140.10860.0121-0.00480.06580.00460.081134.63561.74962.388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 48
2X-RAY DIFFRACTION2A49 - 259
3X-RAY DIFFRACTION3B3 - 51
4X-RAY DIFFRACTION4B52 - 258

+
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://pdbjlvh1.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