[English] 日本語
Yorodumi
- PDB-4xh5: Crystal structure of Salmonella typhimurium propionate kinase A88... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xh5
TitleCrystal structure of Salmonella typhimurium propionate kinase A88G mutant, in complex with AMPPNP and propionate
ComponentsPropionate kinase
KeywordsTRANSFERASE / KINASE / TDCD mutant / AMPPNP / PROPIONATE
Function / homology
Function and homology information


propionate kinase / propionate kinase activity / L-threonine catabolic process to propionate / acetate kinase activity / acetate metabolic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Propionate kinase / Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...Propionate kinase / Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PROPANOIC ACID / Propionate kinase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsMurthy, A.M. / Mathivanan, S. / Chittori, S. / Savithri, H.S. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DBT India
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism
Authors: Murthy, A.M.V. / Mathivanan, S. / Chittori, S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJan 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6045
Polymers44,8361
Non-polymers7684
Water1,892105
1
A: Propionate kinase
hetero molecules

A: Propionate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,20910
Polymers89,6722
Non-polymers1,5378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8980 Å2
ΔGint-53 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.000, 111.000, 66.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-402-

GOL

21A-402-

GOL

31A-561-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Propionate kinase


Mass: 44835.938 Da / Num. of mol.: 1 / Fragment: UNP residues 4-397 / Mutation: A88G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: tdcD, oxd-2, STM3242 / Plasmid: PRSET C PRSET C PRSETPRSET PRSET C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O06961, propionate kinase

-
Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 30% pentaerythritol ethoxylate, 0.05M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2014
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.11→42.59 Å / Num. obs: 27037 / % possible obs: 99 % / Redundancy: 5.5 % / Rsym value: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 2.11→2.23 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.2 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHASERphasing
SCALAdata scaling
Cootmodel building
iMOSFLM1.0.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E1Y

2e1y


Resolution: 2.11→42.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.745 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23068 1359 5 %RANDOM
Rwork0.17468 ---
obs0.17746 25673 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.994 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.11→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 47 105 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193014
X-RAY DIFFRACTIONr_bond_other_d0.0020.022834
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.9654097
X-RAY DIFFRACTIONr_angle_other_deg0.88436468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10523.492126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37715464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5551521
X-RAY DIFFRACTIONr_chiral_restr0.1050.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02693
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_it3.1113.7691563
X-RAY DIFFRACTIONr_mcbond_other3.1113.7671562
X-RAY DIFFRACTIONr_mcangle_it4.2765.6211948
X-RAY DIFFRACTIONr_mcangle_other4.2755.6231949
X-RAY DIFFRACTIONr_scbond_it4.0244.0321451
X-RAY DIFFRACTIONr_scbond_other4.0224.0331452
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6565.9592150
X-RAY DIFFRACTIONr_long_range_B_refined7.12930.4513405
X-RAY DIFFRACTIONr_long_range_B_other7.12630.4523405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.113→2.168 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 84 -
Rwork0.245 1757 -
obs--91.82 %

+
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