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- PDB-1j3w: Structure of Gliding protein-mglB from Thermus Thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1j3w
TitleStructure of Gliding protein-mglB from Thermus Thermophilus HB8
ComponentsGiding protein-mglB
KeywordsStructural genomics / unknown function / Gliding / Motility / mglB / mutational function / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of TOR signaling / guanyl-nucleotide exchange factor activity / molecular adaptor activity
Similarity search - Function
Ragulator complex protein LAMTOR2-like / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Gliding motility protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsLokanath, N.K. / Kunishima, N. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of Gliding protein-mglB from Thermus THermophilus HB8
Authors: Lokanath, N.K. / Kunishima, N. / Miyano, M.
History
DepositionFeb 18, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Giding protein-mglB
B: Giding protein-mglB
C: Giding protein-mglB
D: Giding protein-mglB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8569
Polymers71,2494
Non-polymers6075
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-77 kcal/mol
Surface area23610 Å2
MethodPISA
2
C: Giding protein-mglB
D: Giding protein-mglB
hetero molecules

C: Giding protein-mglB
D: Giding protein-mglB
hetero molecules

A: Giding protein-mglB
B: Giding protein-mglB
hetero molecules

A: Giding protein-mglB
B: Giding protein-mglB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,71318
Polymers142,4998
Non-polymers1,21410
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
Buried area17130 Å2
ΔGint-106 kcal/mol
Surface area45340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.982, 117.186, 111.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-1305-

MG

21D-1418-

HOH

31D-1419-

HOH

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Components

#1: Protein
Giding protein-mglB


Mass: 17812.338 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9X9L0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.6
Details: 0.1M MES, 0.88M MgSO4, pH 5.6, MICROBATCH, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 27, 2002
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 104540 / Num. obs: 104432 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 10 / Biso Wilson estimate: 16.9 Å2
Reflection shellResolution: 1.5→1.55 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.5→30 Å / Isotropic thermal model: ANISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 5277 -RANDOM
Rwork0.2076 ---
all0.2084 104540 --
obs0.2084 104432 99.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 35 553 4680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.004

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