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- PDB-4zcm: Crystal Structure of Escherichia coli GTPase BipA/TypA Complexed ... -

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Basic information

Entry
Database: PDB / ID: 4zcm
TitleCrystal Structure of Escherichia coli GTPase BipA/TypA Complexed with ppGpp
ComponentsGTP-binding protein TypA/BipA
KeywordsGTP-binding protein / BipA / GTPase / Nucleotide
Function / homology
Function and homology information


guanosine tetraphosphate binding / protein folding chaperone / response to cold / ribosome binding / response to heat / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / rRNA binding / translation ...guanosine tetraphosphate binding / protein folding chaperone / response to cold / ribosome binding / response to heat / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / rRNA binding / translation / ribonucleoprotein complex / GTPase activity / GTP binding / cytoplasm / cytosol
Similarity search - Function
GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / : / : / : / : / TypA/BipA C-terminal domain / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 ...GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / : / : / : / : / TypA/BipA C-terminal domain / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / Translation factors / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / COBALT HEXAMMINE(III) / Large ribosomal subunit assembly factor BipA / 50S ribosomal subunit assembly factor BipA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsFan, H.T. / Hahm, J. / Diggs, S. / Blaha, G.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli.
Authors: Fan, H. / Hahm, J. / Diggs, S. / Perry, J.J. / Blaha, G.
History
DepositionApr 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 2, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein TypA/BipA
B: GTP-binding protein TypA/BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,88410
Polymers141,9852
Non-polymers1,8998
Water00
1
A: GTP-binding protein TypA/BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9425
Polymers70,9921
Non-polymers9504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein TypA/BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9425
Polymers70,9921
Non-polymers9504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.821, 160.125, 89.718
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GTP-binding protein TypA/BipA / Tyrosine phosphorylated protein A


Mass: 70992.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: typA, bipA, yihK, b3871, JW5571 / Production host: Escherichia coli (E. coli) / References: UniProt: P32132, UniProt: P0DTT0*PLUS
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl, 2 % PEG 6000, and 5 mM [Co(NH3)6]Cl3, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.31→48.471 Å / Num. obs: 23655 / % possible obs: 98.9 % / Redundancy: 3 % / Biso Wilson estimate: 70.4 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 7
Reflection shellResolution: 3.31→3.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.8 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Cootmodel building
MOLREPphasing
PHENIXdev_1819refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCI

4zci


Resolution: 3.31→48.471 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2911 1128 4.78 %
Rwork0.2326 --
obs0.2354 23602 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104 Å2
Refinement stepCycle: LAST / Resolution: 3.31→48.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8477 0 102 0 8579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058711
X-RAY DIFFRACTIONf_angle_d1.02311872
X-RAY DIFFRACTIONf_dihedral_angle_d16.2113144
X-RAY DIFFRACTIONf_chiral_restr0.0361367
X-RAY DIFFRACTIONf_plane_restr0.0041556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3097-3.46030.36791440.28922767X-RAY DIFFRACTION100
3.4603-3.64270.34281520.27512798X-RAY DIFFRACTION99
3.6427-3.87080.32371270.25182796X-RAY DIFFRACTION99
3.8708-4.16950.271350.23562816X-RAY DIFFRACTION100
4.1695-4.58890.27881500.21082782X-RAY DIFFRACTION100
4.5889-5.25220.28481420.2042826X-RAY DIFFRACTION100
5.2522-6.61450.28611380.25932816X-RAY DIFFRACTION100
6.6145-48.4760.26331400.2092873X-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)
12.5077-1.55980.30091.44650.3691.0532-0.1275-0.02610.32290.13550.07750.1026-0.06180.0566-0.01220.13480.06230.09120.5936-0.01010.70142.79490.002814.105
21.6974-1.1808-0.3632.75190.15771.3521-0.12460.0804-0.16370.33510.2961-0.22820.092-0.06720.05170.26320.06940.05170.62190.00270.627117.0619-8.749318.0255
31.9596-0.7787-1.19862.21640.21283.0075-0.0193-0.31090.26530.81670.37310.00711.27480.48650.03691.22020.2709-0.08420.7432-0.09660.64220.24725.550249.5792
41.69380.463-0.28140.8370.22160.2285-0.6354-0.59850.2472-0.55680.4710.3859-0.1333-0.0168-0.00331.1051-0.1303-0.20110.68150.00180.69912.3939-41.138432.4602
52.33430.9639-0.89081.58880.21211.7739-0.4704-0.5733-0.0002-0.34260.26360.08560.16620.1051-0.00730.95220.0537-0.18410.6426-0.00060.657110.9039-40.3531.3413
60.3532-0.04730.33870.0736-0.27151.13180.06920.06740.20850.29610.05420.0402-1.34490.6681-1.13762.7621-0.64170.34591.2336-0.27390.827418.115-39.66384.3623
71.41690.6979-0.56641.22481.11862.33790.677-0.1708-0.0482-0.1423-0.0481-0.0872-0.92880.15680.01821.3496-0.26840.06930.76240.00890.72285.3421-53.2744-4.9265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 161 )
2X-RAY DIFFRACTION2chain 'A' and (resid 162 through 327 )
3X-RAY DIFFRACTION3chain 'A' and (resid 328 through 601 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 118 )
5X-RAY DIFFRACTION5chain 'B' and (resid 119 through 327 )
6X-RAY DIFFRACTION6chain 'B' and (resid 328 through 375 )
7X-RAY DIFFRACTION7chain 'B' and (resid 376 through 601 )

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