[English] 日本語
Yorodumi
- PDB-5ckw: Crystal structure of LegK4_AMPPNP Kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ckw
TitleCrystal structure of LegK4_AMPPNP Kinase
ComponentsLegK4
KeywordsTRANSFERASE / Legionella / Bacterial effectors / serine/threonine kinase / type IV secretion system
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein phosphorylation / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsFlayhan, A. / Terradot, L.
CitationJournal: Sci Rep / Year: 2015
Title: The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase.
Authors: Flayhan, A. / Berge, C. / Bailo, N. / Doublet, P. / Bayliss, R. / Terradot, L.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: LegK4
A: LegK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,31610
Polymers102,1262
Non-polymers1,1908
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-65 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.684, 76.871, 86.441
Angle α, β, γ (deg.)90.00, 98.19, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein LegK4


Mass: 51063.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (strain Lens) (bacteria)
Gene: lpl0262 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5WZW9
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 10% (w/v) polyethylene glycol (PEG) 20000, 20% (w/v) PEG 550 mono-methyl ether, 30 mM MgCl2, 30 mM CaCl2 and 100 mM Tris/Bicine pH 8.3.

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 37547 / % possible obs: 99.42 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.1149 / Net I/σ(I): 11.14
Reflection shellResolution: 2.49→2.579 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.7 / Num. measured obs: 12847 / Num. unique all: 3570 / CC1/2: 0.6 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CLR

5clr


Resolution: 2.49→40.347 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 1878 5 %
Rwork0.2037 --
obs0.2066 37542 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.49→40.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6218 0 68 192 6478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096399
X-RAY DIFFRACTIONf_angle_d1.3498647
X-RAY DIFFRACTIONf_dihedral_angle_d18.3182405
X-RAY DIFFRACTIONf_chiral_restr0.0521000
X-RAY DIFFRACTIONf_plane_restr0.0061071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4901-2.55740.30441370.27242592X-RAY DIFFRACTION94
2.5574-2.63260.29991430.262726X-RAY DIFFRACTION100
2.6326-2.71760.32841430.25472707X-RAY DIFFRACTION100
2.7176-2.81470.3261450.25522771X-RAY DIFFRACTION100
2.8147-2.92730.35381440.24752720X-RAY DIFFRACTION100
2.9273-3.06050.31521450.24282770X-RAY DIFFRACTION100
3.0605-3.22180.30971450.24122744X-RAY DIFFRACTION100
3.2218-3.42360.28261440.2292733X-RAY DIFFRACTION100
3.4236-3.68770.271440.19892736X-RAY DIFFRACTION100
3.6877-4.05850.22831460.17162774X-RAY DIFFRACTION100
4.0585-4.64510.20311460.16262786X-RAY DIFFRACTION100
4.6451-5.84950.20521460.17542775X-RAY DIFFRACTION100
5.8495-40.35190.22931500.18122830X-RAY DIFFRACTION100
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)
11.3480.00510.46640.74120.64851.32540.05580.28960.2428-0.34460.058-0.1714-0.13890.0625-0.22441.28080.06490.32430.4872-0.0290.48586.5994-9.6815-11.0386
21.7517-0.0674-1.00981.09590.1912.94050.1008-0.00840.231-0.14660.0747-0.1796-0.2979-0.08330.07221.4128-0.00060.35170.4056-0.0810.35280.8682-4.6505-3.3027
31.4627-0.357-0.37441.06270.26990.9940.178-0.04380.0514-0.74850.0846-0.1493-0.1412-0.0054-0.06540.5225-0.10230.13030.2947-0.0140.1913-6.3003-6.924122.3413
41.6786-0.19960.03131.3761-0.28030.7594-0.2679-0.3509-0.3698-0.16290.4343-0.190.08220.3637-0.04130.2259-0.00960.11860.4981-0.0450.401110.3367-24.551243.5396
51.12120.355-0.540.33540.33091.40520.18630.5344-0.316-0.48240.15460.00080.1343-0.1378-0.2751.48940.0904-0.70090.87130.1171.5313-48.9052-25.9918-9.6522
61.27670.50791.32751.98840.31292.0305-0.25050.52080.0376-0.3517-0.0119-0.2207-0.28710.27760.08581.41160.0242-0.97420.7216-0.08791.5904-41.3031-32.8011-5.2865
71.5034-1.12250.2162.5158-0.33141.47450.11290.0503-0.2212-0.0812-0.0858-0.05250.34590.3213-0.18281.49380.121-1.1180.52010.22731.6197-40.1488-34.22012.3374
81.04930.3198-0.16751.2506-0.52870.23080.09110.3343-0.5025-0.6403-0.07450.12180.3140.0232-0.57771.3988-0.1027-1.04050.472-0.02342.041-40.958-41.97545.9591
90.62310.23470.37750.7992-0.04141.13750.3532-0.2841-0.7566-0.69510.25141.16240.455-0.10890.01540.5972-0.1051-0.4340.25630.29631.2083-30.3637-27.949225.5963
103.9159-2.9246-0.56562.47220.71670.6090.1519-0.3446-0.48480.2292-0.20250.1379-0.0729-0.17180.00030.2811-0.09030.05380.60440.26881.1176-41.9715-22.257839.0326
114.8207-0.1615-0.28264.5486-0.65263.15080.0801-1.0266-0.75410.369-0.5288-0.24470.18620.21940.12220.4633-0.11590.30810.77450.14741.0478-53.0397-17.193950.23
125.0723-0.48270.0940.42060.66391.95750.0664-0.9076-0.12610.4138-0.3403-0.1024-0.10370.16740.00150.3894-0.05610.1380.68240.25870.9904-43.3658-11.53647.3176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 58 )
2X-RAY DIFFRACTION2chain 'B' and (resid 59 through 105 )
3X-RAY DIFFRACTION3chain 'B' and (resid 106 through 331 )
4X-RAY DIFFRACTION4chain 'B' and (resid 332 through 404 )
5X-RAY DIFFRACTION5chain 'A' and (resid 21 through 49 )
6X-RAY DIFFRACTION6chain 'A' and (resid 50 through 92 )
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 117 )
8X-RAY DIFFRACTION8chain 'A' and (resid 118 through 152 )
9X-RAY DIFFRACTION9chain 'A' and (resid 153 through 305 )
10X-RAY DIFFRACTION10chain 'A' and (resid 306 through 352 )
11X-RAY DIFFRACTION11chain 'A' and (resid 353 through 371 )
12X-RAY DIFFRACTION12chain 'A' and (resid 372 through 404 )

+
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