[English] 日本語
Yorodumi
- PDB-4itl: Crystal structure of LpxK from Aquifex aeolicus in complex with A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4itl
TitleCrystal structure of LpxK from Aquifex aeolicus in complex with AMP-PCP at 2.1 angstrom resolution
ComponentsTetraacyldisaccharide 4'-kinase
KeywordsTRANSFERASE / membrane protein / kinase / lipid A / P-loop / P-loop containing nucleoside triphosphate hydrolase / disaccharide-1-phosphate 4'-kinase / membrane / lipid metabolism / tetraacyldisaccharide 4'-kinase
Function / homology
Function and homology information


tetraacyldisaccharide 4'-kinase / lipid-A 4'-kinase activity / lipopolysaccharide core region biosynthetic process / lipid A biosynthetic process / ATP binding / plasma membrane
Similarity search - Function
Tetraacyldisaccharide 4'-kinase / Tetraacyldisaccharide-1-P 4'-kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Tetraacyldisaccharide 4'-kinase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsEmptage, R.P. / Pemble IV, C.W. / York, J.D. / Raetz, C.R.H. / Zhou, P.
CitationJournal: Biochemistry / Year: 2013
Title: Mechanistic Characterization of the Tetraacyldisaccharide-1-phosphate 4'-Kinase LpxK Involved in Lipid A Biosynthesis.
Authors: Emptage, R.P. / Pemble, C.W. / York, J.D. / Raetz, C.R. / Zhou, P.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Tetraacyldisaccharide 4'-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3795
Polymers36,5981
Non-polymers7814
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.086, 75.372, 104.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Tetraacyldisaccharide 4'-kinase / Lipid A 4'-kinase


Mass: 36597.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: lpxK, aq_1656 / Production host: Escherichia coli (E. coli)
References: UniProt: O67572, tetraacyldisaccharide 4'-kinase
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES, MPD, NaCl, DDM, Glycerol, EDTA, AMP-PCP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 23, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. all: 31533 / Num. obs: 29108 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.059 / Χ2: 2.155 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.143.10.3919791.117162.8
2.14-2.183.50.41910241.05167.2
2.18-2.223.70.35111421.064173.6
2.22-2.263.90.30712131.105178.5
2.26-2.3140.28213501.161187
2.31-2.374.20.27214291.123191.7
2.37-2.424.40.22315011.188196.2
2.42-2.494.60.20515361.242199.4
2.49-2.564.80.17715531.277199.9
2.56-2.654.90.15415811.4651100
2.65-2.7450.13515451.5561100
2.74-2.854.90.10115781.641100
2.85-2.984.90.08715591.9481100
2.98-3.144.90.07415862.217199.9
3.14-3.334.80.0615752.644199.8
3.33-3.594.70.05715813.156199.7
3.59-3.954.60.05315793.71199.6
3.95-4.524.50.04915953.983199.3
4.52-5.74.40.04816074.031198.6
5.7-5040.0515954.196191.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1066refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EHY

4ehy


Resolution: 2.09→35.453 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1901 2000 7.25 %RANDOM
Rwork0.167 ---
all0.1688 27588 --
obs0.1688 27588 87.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.32 Å2 / Biso mean: 50.2557 Å2 / Biso min: 15.25 Å2
Refinement stepCycle: LAST / Resolution: 2.09→35.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 49 55 2631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132631
X-RAY DIFFRACTIONf_angle_d1.523538
X-RAY DIFFRACTIONf_chiral_restr0.083382
X-RAY DIFFRACTIONf_plane_restr0.008439
X-RAY DIFFRACTIONf_dihedral_angle_d16.0251019
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.14230.2609820.21351047112951
2.1423-2.20020.2486970.19981247134461
2.2002-2.26490.22991130.191439155270
2.2649-2.3380.24841270.18761627175479
2.338-2.42160.23131400.18411793193387
2.4216-2.51850.21891510.1781939209093
2.5185-2.63310.21111550.17811976213195
2.6331-2.77190.21521550.18611989214497
2.7719-2.94550.23191600.18582038219898
2.9455-3.17280.24931620.18662069223199
3.1728-3.49180.20151620.17032089225199
3.4918-3.99650.18761650.15822100226599
3.9965-5.03280.1611660.13432122228899
5.0328-35.45860.1581650.17652113227894
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)
12.77870.4851-0.39471.3694-0.24011.4184-0.01730.8780.6297-0.562-0.07080.2577-0.6608-0.1798-0.12520.51130.0478-0.07740.33430.07410.23344.67621.53-22.1801
26.8445-1.6238-1.06122.08-0.49686.3820.1254-0.4005-0.2326-0.04980.0592-0.28830.20390.5744-0.16260.25130.0264-0.01330.24180.00450.296411.9115-12.5599-9.6753
35.39360.11930.37472.7397-0.36124.72340.03710.0026-0.1171-0.1318-0.0331-0.38730.25330.6938-0.02880.21180.05490.00410.2941-0.01730.214716.4814-11.9562-12.7462
42.4570.5804-0.74941.35710.04341.35020.0338-0.08050.2851-0.1670.12320.7029-0.5036-0.7669-0.06680.25210.1371-0.03860.48590.01270.393-4.7845-0.912-10.8735
52.20960.29380.96081.3947-0.04343.5971-0.1877-0.6863-0.06810.28260.14240.1823-0.2218-0.40140.06690.21490.02680.04620.4501-0.0080.25056.894-8.02897.1127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 50 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 81 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 149 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 199 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 200 through 315 )A0

+
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