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- PDB-4zck: Crystal Structure of C-terminal Fragment of Escherichia coli BipA/TypA -

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Basic information

Entry
Database: PDB / ID: 4zck
TitleCrystal Structure of C-terminal Fragment of Escherichia coli BipA/TypA
ComponentsGTP-binding protein TypA/BipA
KeywordsGTP-BINDING PROTEIN / BipA / GTPase / Nucleotide
Function / homology
Function and homology information


guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosomal large subunit assembly / ribosome biogenesis / ribosome binding / tRNA binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding ...guanosine tetraphosphate binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosomal large subunit assembly / ribosome biogenesis / ribosome binding / tRNA binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / cytoplasm / cytosol
Similarity search - Function
bipa protein / : / : / : / : / TypA/BipA C-terminal domain / GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / Elongation Factor G (Translational Gtpase), domain 3 ...bipa protein / : / : / : / : / TypA/BipA C-terminal domain / GTP-binding protein TypA / BipA, domain V / GTP-binding protein TypA/BipA, C-terminal / Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Alpha-Beta Plaits / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
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: 2.48 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0903
Polymers37,0411
Non-polymers492
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-15 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.562, 83.562, 191.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 37040.930 Da / Num. of mol.: 1 / Fragment: UNP residues 306-603
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 4.52 Å3/Da / Density % sol: 72.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 3.04 M sodium formate, 200 mM Tris-HCl, and 1 mM magnesium bromide, pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.48→48 Å / Num. obs: 24915 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 70.4 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.5
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
Cootmodel building
PHENIXdev_1819refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E3X

3e3x


Resolution: 2.48→48 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 1268 5.1 %
Rwork0.1944 --
obs0.1961 24846 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86 Å2
Refinement stepCycle: LAST / Resolution: 2.48→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 0 33 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012367
X-RAY DIFFRACTIONf_angle_d1.2863185
X-RAY DIFFRACTIONf_dihedral_angle_d15.318899
X-RAY DIFFRACTIONf_chiral_restr0.052356
X-RAY DIFFRACTIONf_plane_restr0.005424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.57930.41531370.36192503X-RAY DIFFRACTION98
2.5793-2.69670.33091320.33872592X-RAY DIFFRACTION100
2.6967-2.83880.35981330.30742570X-RAY DIFFRACTION100
2.8388-3.01670.29771280.24882599X-RAY DIFFRACTION100
3.0167-3.24950.27841580.23272564X-RAY DIFFRACTION100
3.2495-3.57650.26541400.20832615X-RAY DIFFRACTION100
3.5765-4.09370.19651400.16852631X-RAY DIFFRACTION100
4.0937-5.15670.16861470.15452669X-RAY DIFFRACTION100
5.1567-47.96920.21431530.17712835X-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)
14.91890.7212-1.44354.65440.92016.9777-0.10330.9107-0.0979-0.56060.24060.430.1172-1.0308-0.20710.64340.0744-0.05461.06780.15730.6645-15.4447-13.1816-41.5999
23.9348-0.3257-2.20683.91291.89987.10090.08330.54870.3564-0.3350.32250.8651-0.527-1.1612-0.2660.49010.08930.06740.94060.16440.6297-15.9976-11.4548-32.035
35.5982-1.78410.35068.4748-2.82829.40720.28650.10550.30050.4787-0.2423-0.2804-0.08760.2663-0.07080.3595-0.04020.02970.5354-0.04580.4045-12.4462-15.5608-10.8467
46.29580.8938-2.99150.9841-0.76953.2510.3987-0.0110.85430.0825-0.04530.0459-0.4608-0.0804-0.38330.65490.05730.00980.6258-0.00330.56642.838-8.7182-26.9601
56.3527-4.2859-0.87853.25290.38844.8831-0.034-0.60581.0549-0.07610.0625-0.5926-0.42841.1029-0.13330.7098-0.05040.01530.8725-0.0840.634620.6445-12.1075-28.7004
64.69510.3253-1.68652.9763-0.90038.14320.42210.28080.53150.0115-0.0039-0.0998-1.2589-0.4639-0.49230.60550.13320.15990.74010.0470.6661-0.9177-5.3967-35.6067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 304 through 354 )
2X-RAY DIFFRACTION2chain 'A' and (resid 355 through 394 )
3X-RAY DIFFRACTION3chain 'A' and (resid 395 through 459 )
4X-RAY DIFFRACTION4chain 'A' and (resid 460 through 535 )
5X-RAY DIFFRACTION5chain 'A' and (resid 536 through 564 )
6X-RAY DIFFRACTION6chain 'A' and (resid 565 through 603 )

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