[English] 日本語
Yorodumi
- PDB-4m7x: Staphylococcus aureus Type II pantothenate kinase in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m7x
TitleStaphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog
ComponentsType II pantothenate kinase
KeywordsTRANSFERASE/TRANSFERASE inhibitor / pantothenate kinase / inhibitor / antibacterial / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / cytosol
Similarity search - Function
Type II pantothenate kinase, bacterial / Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-27Q / ADENOSINE-5'-DIPHOSPHATE / Type II pantothenate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsMottaghi, K. / Hong, B. / Tempel, W. / Park, H.
CitationJournal: ACS Infect Dis / Year: 2016
Title: Discovery of Potent Pantothenamide Inhibitors of Staphylococcus aureus Pantothenate Kinase through a Minimal SAR Study: Inhibition Is Due to Trapping of the Product.
Authors: Hughes, S.J. / Barnard, L. / Mottaghi, K. / Tempel, W. / Antoshchenko, T. / Hong, B.S. / Allali-Hassani, A. / Smil, D. / Vedadi, M. / Strauss, E. / Park, H.W.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Sep 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 / 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 / _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.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.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.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_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: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,80416
Polymers29,9561
Non-polymers84815
Water2,630146
1
A: Type II pantothenate kinase
hetero molecules

A: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,60732
Polymers59,9122
Non-polymers1,69630
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7260 Å2
ΔGint-80 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.920, 136.530, 73.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 29955.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: MW2 / Gene: coaW, MW2054 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-TR / References: UniProt: Q8NVG0, pantothenate kinase

-
Non-polymers , 5 types, 161 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#5: Chemical ChemComp-27Q / N-heptyl-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 396.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H33N2O7P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.4 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.5
Details: 0.01 M inhibitor, 0.01 M magnesium chloride, 0.01 M ATP were added to the protein sample. 30% PEG4000, 0.2M magnesium chloride, 0.1M Tris hydrochloride, pH 8.5, vapor diffusion, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.42→68.265 Å / Num. all: 53304 / Num. obs: 53304 / % possible obs: 98.1 % / Redundancy: 9.7 % / Rsym value: 0.086 / Net I/σ(I): 14.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.42-1.57.50.7361.15657675690.73696.5
1.5-1.597.50.4251.85369371920.42596.9
1.59-1.77.50.262.95092568160.2697.5
1.7-1.837.40.1734.24769564170.17397.9
1.83-2.017.60.1274.64483159050.12798.5
2.01-2.2514.20.1743.37665253970.17498.8
2.25-2.5913.90.11656711648280.11699.3
2.59-3.1813.50.0827.35536441130.08299.7
3.18-4.4912.80.06694119832150.06699.8
4.49-36.8111.60.053112140618520.05398.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.7.0027refinement
PDB_EXTRACT3.12data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EWS

2ews


Resolution: 1.42→35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.912 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: GEOMETRY RESTRAINTS FOR THE INHIBITOR WERE CALCULATED BY PRODRG, AND MODIFIED BASED ON DATA IN THE CAMBRIDGE STRUCTURAL DATABASE. COOT WAS USED FOR MODEL BUILDING. THE MOLPROBITY SERVER WAS ...Details: GEOMETRY RESTRAINTS FOR THE INHIBITOR WERE CALCULATED BY PRODRG, AND MODIFIED BASED ON DATA IN THE CAMBRIDGE STRUCTURAL DATABASE. COOT WAS USED FOR MODEL BUILDING. THE MOLPROBITY SERVER WAS USED FOR MODEL GEOMETRY VALIDATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 2711 5.086 %RANDOM
Rwork0.1713 ---
obs0.172 53298 97.882 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 75.12 Å2 / Biso mean: 23.781 Å2 / Biso min: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.095 Å20 Å20 Å2
2---1.069 Å20 Å2
3---1.164 Å2
Refinement stepCycle: LAST / Resolution: 1.42→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 66 146 2266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022245
X-RAY DIFFRACTIONr_bond_other_d0.0060.022138
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9653072
X-RAY DIFFRACTIONr_angle_other_deg1.013.0074901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6175296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95624.4998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.51615352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.234159
X-RAY DIFFRACTIONr_chiral_restr0.090.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.4570.2612160.2663597396196.264
1.457-1.4970.231990.2293541388596.268
1.497-1.540.2311760.1933484379096.57
1.54-1.5870.2341770.1813349363597.001
1.587-1.6390.1881810.1683266355197.071
1.639-1.6970.2091780.1593172343897.44
1.697-1.7610.1861470.1623130335797.617
1.761-1.8320.1991520.1672985320797.817
1.832-1.9130.1781540.1652856306498.238
1.913-2.0070.1711560.1682738294598.268
2.007-2.1150.1661340.162651282598.584
2.115-2.2420.2091300.1692484264698.791
2.242-2.3970.1821440.1652347251699.006
2.397-2.5880.1771290.1752199234499.317
2.588-2.8330.1911160.1732036216599.4
2.833-3.1650.2031030.1811859196999.644
3.165-3.6490.22740.1731660174099.655
3.649-4.4580.172620.1461434150099.733
4.458-6.2530.171470.1681142119199.832
6.253-350.236360.19365571696.508
Refinement TLS params.Method: refined / Origin x: 17.532 Å / Origin y: 13.8455 Å / Origin z: -3.5562 Å
111213212223313233
T0.0126 Å20.0002 Å2-0.0003 Å2-0.0277 Å20.0037 Å2--0.0236 Å2
L0.8446 °2-0.3436 °2-0.0446 °2-1.5198 °20.0905 °2--0.575 °2
S0.0447 Å °0.0333 Å °0.1227 Å °-0.0782 Å °-0.0698 Å °0.0267 Å °-0.0677 Å °-0.01 Å °0.0251 Å °

+
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