[English] 日本語
Yorodumi
- PDB-3nku: Crystal structure of the N-terminal domain of DrrA/SidM from Legi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nku
TitleCrystal structure of the N-terminal domain of DrrA/SidM from Legionella pneumophila
ComponentsDrrA
KeywordsPROTEIN TRANSPORT / POSTTRANSLATIONAL MODIFICATION / AMPYLATION / ADENYLYLATION / RAB1B / RAB1 / DRRA / SIDM / VESICULAR TRANSPORT
Function / homology
Function and homology information


: / protein guanylylation / AMPylase activity / protein adenylyltransferase / protein adenylylation / host cell cytoplasmic vesicle / phosphatidylinositol-4-phosphate binding / regulation of GTPase activity / guanyl-nucleotide exchange factor activity / host cell cytoplasmic vesicle membrane ...: / protein guanylylation / AMPylase activity / protein adenylyltransferase / protein adenylylation / host cell cytoplasmic vesicle / phosphatidylinositol-4-phosphate binding / regulation of GTPase activity / guanyl-nucleotide exchange factor activity / host cell cytoplasmic vesicle membrane / small GTPase binding / protein guanylyltransferase activity / extracellular region / ATP binding / membrane
Similarity search - Function
Tetracycline Repressor; domain 2 - #170 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / Tetracycline Repressor; domain 2 ...Tetracycline Repressor; domain 2 - #170 / DrrA guanine nucleotide-exchange factor domain / : / : / SidM, Rab1-activation domain / SidM, N-terminal domain / DrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / Tetracycline Repressor; domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Multifunctional virulence effector protein DrrA
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsMueller, M.P. / Peters, H. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
CitationJournal: Science / Year: 2010
Title: The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b.
Authors: Muller, M.P. / Peters, H. / Blumer, J. / Blankenfeldt, W. / Goody, R.S. / Itzen, A.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DrrA
B: DrrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3594
Polymers49,1032
Non-polymers2562
Water2,900161
1
A: DrrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8083
Polymers24,5511
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DrrA


Theoretical massNumber of molelcules
Total (without water)24,5511
Polymers24,5511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.609, 49.955, 159.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DrrA / / sidM


Mass: 24551.354 Da / Num. of mol.: 2 / Fragment: N-terminal domain (residues 9-218)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia / Gene: DrrA / Plasmid: pOPIN-NHis-3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q29ST3
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 298 K
Details: 35 - 40% (v/v) PEG600, 0.1 M phosphate/citrate, 3% (w/v) glucose monohydrate, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP
PH range: 4.2 - 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2009 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 16.01 / Number: 221514 / Rmerge(I) obs: 0.154 / D res high: 2.4 Å / Num. obs: 29314 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2047.75296.310.069
15206810010.048
101527610010.05
71077510010.056
6771110010.071
56134810010.079
45310310010.084
34867610010.17
2.93161310010.4
2.82.9180510010.496
2.72.8213610010.615
2.62.7248810010.79
2.52.6287910010.955
2.42.5338410011.229
ReflectionResolution: 2.1→47.7 Å / Num. obs: 23028 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.19 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.56
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementResolution: 2.1→47.7 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.522 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1129 4.9 %RANDOM
Rwork0.18 ---
obs0.182 23028 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--0.08 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 17 161 3146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223064
X-RAY DIFFRACTIONr_bond_other_d0.0010.022117
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9874139
X-RAY DIFFRACTIONr_angle_other_deg0.9713.0015170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56325.811148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.31515552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8851514
X-RAY DIFFRACTIONr_chiral_restr0.1020.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
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_it1.1181.51891
X-RAY DIFFRACTIONr_mcbond_other0.3071.5751
X-RAY DIFFRACTIONr_mcangle_it2.05723053
X-RAY DIFFRACTIONr_scbond_it3.63231173
X-RAY DIFFRACTIONr_scangle_it5.8084.51082
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 80 -
Rwork0.167 1601 -
obs--99.82 %
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)
12.0911.2060.42692.77010.55411.6120.0703-0.2159-0.12010.12080.17510.01010.1148-0.0793-0.24550.09450.0241-0.05160.11290.04490.07342.117216.476535.8773
21.148-0.012-0.04880.7833-0.38070.74020.024-0.01910.02710.06250.0242-0.0511-0.0141-0.0178-0.04810.03360.0021-0.00420.0317-0.00760.014737.698237.0315.6648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

+
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