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- PDB-4p3y: Crystal structure of Acinetobacter baumannii DsbA in complex with... -

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Basic information

Entry
Database: PDB / ID: 4p3y
TitleCrystal structure of Acinetobacter baumannii DsbA in complex with EF-Tu
Components
  • Elongation factor Tu 1EF-Tu
  • Thiol:disulfide interchange protein
KeywordsTRANSLATION/OXIDOREDUCTASE / Thioredoxin related / Disulfide oxidase DsbA / Multidrug resistance / disulfide bond formation / Anti-biofilm formation / Antivirulence / bacterial infection / Translation-OXIDOREDUCTASE complex
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / protein-disulfide reductase activity / translation elongation factor activity / isomerase activity / periplasmic space / response to antibiotic / GTPase activity / GTP binding ...guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / protein-disulfide reductase activity / translation elongation factor activity / isomerase activity / periplasmic space / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm
Similarity search - Function
Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors ...Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / 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. / Thioredoxin domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Small GTP-binding protein domain / Thioredoxin-like superfamily / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor Tu / Thiol:disulfide interchange protein / Elongation factor Tu 1
Similarity search - Component
Biological speciesAcinetobacter baumannii AYE (bacteria)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.154 Å
AuthorsPremkumar, L. / Martin, J.L.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL0992138 Australia
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of the Acinetobacter baumannii Dithiol Oxidase DsbA Bound to Elongation Factor EF-Tu Reveals a Novel Protein Interaction Site.
Authors: Premkumar, L. / Kurth, F. / Duprez, W. / Grftehauge, M.K. / King, G.J. / Halili, M.A. / Heras, B. / Martin, J.L.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Mar 1, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_ref / struct_ref_seq / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_nat.pdbx_organism_scientific / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_site_gen.auth_seq_id
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor Tu 1
B: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5055
Polymers63,9452
Non-polymers5603
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-20 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.318, 78.190, 122.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Elongation factor Tu 1 / EF-Tu / EF-Tu 1 / Bacteriophage Q beta RNA-directed RNA polymerase subunit III / P-43


Mass: 43340.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / References: UniProt: P0CE47, UniProt: A0A140N6W0*PLUS
#2: Protein Thiol:disulfide interchange protein


Mass: 20604.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii AYE (bacteria) / Strain: AYE / Gene: dsbA, ABAYE3833 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0V5X3

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Non-polymers , 4 types, 248 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: KCl, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: BLUE ICE
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2012
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→74.32 Å / Num. obs: 39200 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.5 / % possible all: 98.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EFC

1efc


Resolution: 2.154→65.949 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1959 5.01 %Random
Rwork0.1698 ---
obs0.1721 39133 99.27 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.154→65.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4416 0 35 245 4696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084594
X-RAY DIFFRACTIONf_angle_d1.176247
X-RAY DIFFRACTIONf_dihedral_angle_d15.1211719
X-RAY DIFFRACTIONf_chiral_restr0.043699
X-RAY DIFFRACTIONf_plane_restr0.005807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.154-2.20790.28631400.23862570X-RAY DIFFRACTION97
2.2079-2.26760.30481230.24992601X-RAY DIFFRACTION99
2.2676-2.33440.27221630.2212620X-RAY DIFFRACTION100
2.3344-2.40970.25991310.22262636X-RAY DIFFRACTION100
2.4097-2.49590.27281370.21362623X-RAY DIFFRACTION100
2.4959-2.59580.27341320.20612674X-RAY DIFFRACTION100
2.5958-2.71390.28221390.20732628X-RAY DIFFRACTION99
2.7139-2.8570.25411400.1912657X-RAY DIFFRACTION100
2.857-3.0360.26931300.19082663X-RAY DIFFRACTION100
3.036-3.27040.21271230.1852696X-RAY DIFFRACTION100
3.2704-3.59950.2321520.16272629X-RAY DIFFRACTION99
3.5995-4.12030.18151540.14662641X-RAY DIFFRACTION98
4.1203-5.19080.14961320.12072720X-RAY DIFFRACTION99
5.1908-65.97970.17781630.14942816X-RAY DIFFRACTION99
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)
11.806-0.53720.16890.706-0.26480.94460.0265-0.15170.00390.0515-0.057-0.07960.01460.05120.03060.2491-0.0372-0.01030.20.01120.22228.639-22.735517.3751
22.65290.41730.39343.2307-0.67592.81980.08380.2255-0.0083-0.3575-0.29610.3746-0.0643-0.37860.18460.3580.1021-0.11290.4878-0.21710.454926.23227.744816.7232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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