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- PDB-4uaq: Crystal structure of the accessory translocation ATPase, SecA2, f... -

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Basic information

Entry
Database: PDB / ID: 4uaq
TitleCrystal structure of the accessory translocation ATPase, SecA2, from Mycobacterium tuberculosis
ComponentsProtein translocase subunit SecA 2
KeywordsPROTEIN TRANSPORT / DEAD/DEAH box helicase Preprotein translocation ATP binding SecA preprotein cross-linking domain / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


ABC-type protein transporter activity / biological process involved in interaction with host => GO:0051701 / symbiont-mediated perturbation of host immune response / Tolerance of reactive oxygen produced by macrophages / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / cell wall / plasma membrane => GO:0005886 ...ABC-type protein transporter activity / biological process involved in interaction with host => GO:0051701 / symbiont-mediated perturbation of host immune response / Tolerance of reactive oxygen produced by macrophages / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / cell wall / plasma membrane => GO:0005886 / : / protein targeting / Prevention of phagosomal-lysosomal fusion / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Protein translocase subunit SecA, Actinobacteria-type / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain ...Protein translocase subunit SecA, Actinobacteria-type / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein translocase subunit SecA 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSwanson-Smith, S. / Ioerger, T.R. / Rigel, N.W. / Miller, B.K. / Braunstein, M. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
NIH/NIAIDNIHP01AI095208 United States
CitationJournal: J.Bacteriol. / Year: 2015
Title: Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2.
Authors: Swanson, S. / Ioerger, T.R. / Rigel, N.W. / Miller, B.K. / Braunstein, M. / Sacchettini, J.C.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein translocase subunit SecA 2


Theoretical massNumber of molelcules
Total (without water)86,0581
Polymers86,0581
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area33910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.600, 162.090, 67.310
Angle α, β, γ (deg.)90.00, 95.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein translocase subunit SecA 2


Mass: 86057.602 Da / Num. of mol.: 1 / Fragment: UNP residues 31-808
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: secA2, Rv1821, MTCY1A11.22c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGP3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 8000, tris(hydroxymethyl)aminomethane), NaCl, ethylene glycol, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS)

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97949 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 26, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→35.64 Å / Num. obs: 16255 / % possible obs: 78.3 % / Redundancy: 7 % / Biso Wilson estimate: 85.75 Å2 / Rsym value: 0.131 / Net I/σ(I): 14.59
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 0.604 / % possible all: 29.5

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→35.64 Å / Cor.coef. Fo:Fc: 0.9403 / Cor.coef. Fo:Fc free: 0.9122 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 835 5.14 %RANDOM
Rwork0.2115 ---
obs0.2152 16255 --
Displacement parametersBiso mean: 84.86 Å2
Baniso -1Baniso -2Baniso -3
1--12.6151 Å20 Å2-5.0933 Å2
2--4.6661 Å20 Å2
3---7.9489 Å2
Refine analyzeLuzzati coordinate error obs: 0.479 Å
Refinement stepCycle: LAST / Resolution: 2.8→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 0 67 4961
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014968HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.266808HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1553SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes787HARMONIC5
X-RAY DIFFRACTIONt_it4968HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion22.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion720SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5537SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4423 80 5.68 %
Rwork0.3065 1329 -
all0.314 1409 -

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