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- PDB-1mky: Structural Analysis of the Domain Interactions in Der, a Switch P... -

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Basic information

Entry
Database: PDB / ID: 1mky
TitleStructural Analysis of the Domain Interactions in Der, a Switch Protein Containing Two GTPase Domains
ComponentsProbable GTP-binding protein engA
KeywordsLIGAND BINDING PROTEIN / GTPase / EngA / Der / KH-Domain / tandem G-domains
Function / homology
Function and homology information


ribosome biogenesis / ribosome binding / GTP binding
Similarity search - Function
EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / Small GTP-binding protein domain ...EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / Small GTP-binding protein domain / K homology domain-like, alpha/beta / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / GTPase Der
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsRobinson, V.L. / Hwang, J. / Fox, E. / Inouye, M. / Stock, A.M.
Citation
Journal: Structure / Year: 2002
Title: Domain Arrangement of Der, a Switch Protein Containing Two GTPase Domains
Authors: Robinson, V.L. / Hwang, J. / Fox, E. / Inouye, M. / Stock, A.M.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: An essential GTPase, der, containing double GTP-binding domains from Escherichia coli and Thermotoga maritima.
Authors: Hwang, J. / Inouye, M.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 4, 2015Group: Database references / Other
Revision 1.4Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable GTP-binding protein engA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4557
Polymers50,5371
Non-polymers9186
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.137, 77.994, 96.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Probable GTP-binding protein engA


Mass: 50537.117 Da / Num. of mol.: 1 / Fragment: two GTPase domains
Source method: isolated from a genetically manipulated source
Details: probable GTPase / Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): 834(pLysS) / References: UniProt: Q9X1F8
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10
Details: sodium phosphate, potassium phosphate, 3-(cyclohexylamino)-1-propane sulphonic acid (CAPS), pH 10.0, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298K, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.3 M1reservoirNaH2PO4
20.7 M1reservoirK2HPO4
350 mMCAPS1reservoirpH10.0
415 mMbeta-mercaptoethanol1reservoir
526 mg/mlprotein1drop
60.8 M1dropNaH2PO4
70.5 M1dropK2HPO4
850 mMCAPS1droppH10.0
915 mMbeta-mercaptoethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2001
RadiationMonochromator: crystal monochromator + Si mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→19.07 Å / Num. all: 71418 / Num. obs: 69719 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.073 / Net I/σ(I): 26.5
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 10 % / Mean I/σ(I) obs: 6.7 / Num. unique all: 8929 / Rsym value: 0.361 / % possible all: 93.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 44093 / Num. measured all: 465562 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Lowest resolution: 2.01 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.344

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.07 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 6899 -RANDOM
Rwork0.204 ---
all0.208 71418 --
obs0.204 69719 10 %-
Displacement parametersBiso mean: 30.39 Å2 / Baniso 11: 6.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 53 246 3563
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_improper_angle_d0.86
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0.009

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
1.9-1.990.2668210.237831693.1
1.99-2.090.2457940.217862596.1
2.09-2.220.2538710.214868697.1
2.22-2.390.2528540.21875097.9
2.39-2.630.2578820.208880299
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.86
LS refinement shell
*PLUS
Lowest resolution: 2.01 Å / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.239

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