[English] 日本語
Yorodumi
- PDB-4htl: Lmo2764 protein, a putative N-acetylmannosamine kinase, from List... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4htl
TitleLmo2764 protein, a putative N-acetylmannosamine kinase, from Listeria monocytogenes
ComponentsBeta-glucoside kinase
KeywordsTRANSFERASE / structural genomics / sugar kinase / ROK family / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


beta-glucoside kinase / beta-glucoside kinase activity / ATP binding
Similarity search - Function
ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-glucoside kinase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å
AuthorsOsipiuk, J. / Mack, J. / Endres, M. / Salazar, J. / Zhang, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Lmo2764 protein, a putative N-acetylmannosamine kinase, from Listeria monocytogenes.
Authors: Osipiuk, J. / Mack, J. / Endres, M. / Salazar, J. / Zhang, W. / Joachimiak, A.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Beta-glucoside kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8862
Polymers32,8241
Non-polymers621
Water5,693316
1
A: Beta-glucoside kinase
hetero molecules

A: Beta-glucoside kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7724
Polymers65,6482
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area3930 Å2
ΔGint-6 kcal/mol
Surface area23830 Å2
MethodPISA
2
A: Beta-glucoside kinase
hetero molecules

A: Beta-glucoside kinase
hetero molecules

A: Beta-glucoside kinase
hetero molecules

A: Beta-glucoside kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5448
Polymers131,2964
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area13120 Å2
ΔGint-19 kcal/mol
Surface area42390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.694, 121.989, 153.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-429-

HOH

31A-553-

HOH

Detailsdimer based on PISA

-
Components

#1: Protein Beta-glucoside kinase


Mass: 32824.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: bglK, lmo2764 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y3R9, beta-glucoside kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 4, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.64→35.9 Å / Num. all: 49631 / Num. obs: 49631 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.087 / Χ2: 4.171 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.64-1.674.80.6052.124030.83196.7
1.67-1.75.70.54624180.85598.3
1.7-1.736.10.47324420.96798.7
1.73-1.776.40.4124481.05198.7
1.77-1.816.80.35424291.20898.9
1.81-1.857.20.30924771.40199.4
1.85-1.897.90.26124491.65299.4
1.89-1.9480.22824691.91199.6
1.94-280.20124982.32299.8
2-2.0780.16924592.806100
2.07-2.148.20.14725153.22599.9
2.14-2.238.10.13524613.781100
2.23-2.338.20.12325064.312100
2.33-2.458.20.11824824.792100
2.45-2.68.10.10524935.428100
2.6-2.880.09625076.199100
2.8-3.0980.08525157.172100
3.09-3.537.70.07225297.958100
3.53-4.457.60.06225438.471100
4.45-507.50.065258812.09198.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.64→36 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 2.53 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.073 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 2509 5.1 %RANDOM
Rwork0.1277 ---
all0.1298 49630 --
obs0.1298 49630 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.97 Å2 / Biso mean: 29.3068 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.64→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 4 316 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022425
X-RAY DIFFRACTIONr_bond_other_d0.0010.021638
X-RAY DIFFRACTIONr_angle_refined_deg1.461.963308
X-RAY DIFFRACTIONr_angle_other_deg0.9834011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59624.138116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13515416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9961515
X-RAY DIFFRACTIONr_chiral_restr0.1040.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
X-RAY DIFFRACTIONr_rigid_bond_restr3.81934063
X-RAY DIFFRACTIONr_sphericity_free35.649590
X-RAY DIFFRACTIONr_sphericity_bonded18.49654222
LS refinement shellResolution: 1.641→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 170 -
Rwork0.301 3035 -
all-3205 -
obs-3205 90.38 %

+
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