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- PDB-4zci: Crystal Structure of Escherichia coli GTPase BipA/TypA -

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Basic information

Entry
Database: PDB / ID: 4zci
TitleCrystal Structure of Escherichia coli GTPase BipA/TypA
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
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: 2.627 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._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)141,2606
Polymers140,6152
Non-polymers6444
Water1,42379
1
A: GTP-binding protein TypA/BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6303
Polymers70,3081
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein TypA/BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6303
Polymers70,3081
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.717, 161.391, 89.601
Angle α, β, γ (deg.)90.00, 97.95, 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: 70307.547 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: isolated from a genetically manipulated source
Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
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: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2014
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.627→46.004 Å / Num. all: 46793 / Num. obs: 46760 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.4
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 1.4 / % possible all: 96.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PHENIXdev_1819refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CB4, 3E3X

3cb4

3e3x


Resolution: 2.627→46.004 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 2258 4.83 %
Rwork0.2104 --
obs0.2123 46733 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78 Å2
Refinement stepCycle: LAST / Resolution: 2.627→46.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8582 0 0 79 8661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038711
X-RAY DIFFRACTIONf_angle_d0.74411833
X-RAY DIFFRACTIONf_dihedral_angle_d15.63208
X-RAY DIFFRACTIONf_chiral_restr0.0291360
X-RAY DIFFRACTIONf_plane_restr0.0031561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.627-2.68410.38881290.33652123X-RAY DIFFRACTION76
2.6841-2.74650.33971370.30652826X-RAY DIFFRACTION99
2.7465-2.81520.29311430.27762807X-RAY DIFFRACTION100
2.8152-2.89130.29851440.28432810X-RAY DIFFRACTION100
2.8913-2.97640.34711360.27192828X-RAY DIFFRACTION100
2.9764-3.07240.27641490.24752776X-RAY DIFFRACTION100
3.0724-3.18220.28331330.24722856X-RAY DIFFRACTION100
3.1822-3.30960.24571390.24952819X-RAY DIFFRACTION100
3.3096-3.46020.31061340.24742814X-RAY DIFFRACTION100
3.4602-3.64250.25061330.22792836X-RAY DIFFRACTION100
3.6425-3.87060.2631420.21562814X-RAY DIFFRACTION100
3.8706-4.16930.24181540.1862809X-RAY DIFFRACTION100
4.1693-4.58850.19521360.16582822X-RAY DIFFRACTION100
4.5885-5.25170.20441530.16722836X-RAY DIFFRACTION100
5.2517-6.61340.26131420.21362841X-RAY DIFFRACTION100
6.6134-46.01070.21621540.17582858X-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)
16.0394-1.94810.00992.0269-0.01381.3972-0.21980.2678-0.24880.05990.12860.0109-0.0380.12890.08720.2775-0.0049-0.03460.4972-0.04890.34615.264.75019.5103
21.147-0.16181.04930.2129-0.70286.20310.19040.07250.16830.140.1294-0.0237-1.1832-0.2284-0.27570.78580.0610.07620.57140.06650.522313.3904-3.880347.1953
38.13242.56730.3563.5504-0.58942.2491-0.6067-0.10290.5456-0.04480.2893-0.01270.0690.08320.20510.32670.0401-0.04570.4461-0.03750.433719.623945.730130.2213
47.91452.53450.56132.74740.78731.5457-0.1941-0.49740.20670.1812-0.03730.18730.3079-0.0940.23630.39590.05910.09670.44560.00090.34194.642236.02833.1239
51.1548-0.5667-0.8150.28750.31871.1748-0.97910.3599-0.5962-1.23950.66690.38291.6993-0.29010.55521.8938-0.6590.18090.91010.08020.80659.023639.3398-0.3296
61.95971.0396-1.00991.475-0.94054.7674-0.0812-0.0181-0.0598-0.51920.27330.06711.559-0.4673-0.05690.9375-0.1558-0.09750.66290.11150.555623.342252.5181-5.5411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 295 )
2X-RAY DIFFRACTION2chain 'A' and (resid 296 through 601 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 160 )
4X-RAY DIFFRACTION4chain 'B' and (resid 161 through 294 )
5X-RAY DIFFRACTION5chain 'B' and (resid 295 through 345 )
6X-RAY DIFFRACTION6chain 'B' and (resid 346 through 601 )

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