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

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Basic information

Entry
Database: PDB / ID: 4zcl
TitleCrystal Structure of Escherichia coli GTPase BipA/TypA Complexed with GDP
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'-DIPHOSPHATE / 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: 3.06 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)142,1709
Polymers140,6152
Non-polymers1,5557
Water00
1
A: GTP-binding protein TypA/BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0975
Polymers70,3081
Non-polymers7904
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTP-binding protein TypA/BipA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0734
Polymers70,3081
Non-polymers7653
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.430, 160.010, 90.020
Angle α, β, γ (deg.)90.00, 97.70, 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: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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: 2.84 Å3/Da / Density % sol: 56.61 %
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: 3.06→48.181 Å / Num. obs: 29871 / % possible obs: 99.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 72.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.6
Reflection shellResolution: 3.06→3.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
PHENIXdev_1819refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZCI

4zci


Resolution: 3.06→48.181 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 1447 4.85 %
Rwork0.2323 --
obs0.2342 29815 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96 Å2
Refinement stepCycle: LAST / Resolution: 3.06→48.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 0 0 8524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038655
X-RAY DIFFRACTIONf_angle_d0.74111797
X-RAY DIFFRACTIONf_dihedral_angle_d14.5433131
X-RAY DIFFRACTIONf_chiral_restr0.0281368
X-RAY DIFFRACTIONf_plane_restr0.0031550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.16940.35411420.31652817X-RAY DIFFRACTION100
3.1694-3.29620.32041600.31072813X-RAY DIFFRACTION100
3.2962-3.44620.37081320.28972823X-RAY DIFFRACTION100
3.4462-3.62780.32511580.26252823X-RAY DIFFRACTION100
3.6278-3.8550.29661370.26122836X-RAY DIFFRACTION100
3.855-4.15250.2991320.23682837X-RAY DIFFRACTION100
4.1525-4.57010.25081560.20882829X-RAY DIFFRACTION100
4.5701-5.23080.24511720.19662828X-RAY DIFFRACTION100
5.2308-6.58750.26461450.23472837X-RAY DIFFRACTION100
6.5875-48.18680.19311130.19672925X-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)
16.1991-1.8325-0.13213.63110.95512.4034-0.16450.32240.35810.00410.06740.1274-0.08010.02060.09140.16050.01690.04710.49750.09930.50551.3218-0.191812.5552
22.9782-1.31190.0123.2011-0.81361.3345-0.21220.1631-0.01350.17150.2142-0.50180.0591-0.0560.04650.1390.05290.03860.5842-0.06180.627921.9614-10.17916.4339
32.4014-0.7404-0.88052.5675-0.17153.9188-0.1758-0.17120.01571.13360.3992-0.10421.24530.5835-0.1931.46010.3552-0.04430.8161-0.14720.53280.50814.367650.0083
45.37832.4249-1.57282.6179-0.96991.5913-0.693-0.58860.1004-0.61280.38960.24930.35950.06880.28841.03740.0677-0.19090.5835-0.01340.4366.9635-40.833734.9258
51.75370.35070.61261.10861.16353.05490.6392-0.27050.22570.32110.0009-0.1062-1.56810.2807-0.29071.8898-0.42790.20310.7716-0.00590.62698.7486-49.6208-2.6781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 183 )
2X-RAY DIFFRACTION2chain 'A' and (resid 184 through 313 )
3X-RAY DIFFRACTION3chain 'A' and (resid 314 through 601 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 295 )
5X-RAY DIFFRACTION5chain 'B' and (resid 296 through 601 )

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