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- PDB-1nl3: CRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM M... -

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Basic information

Entry
Database: PDB / ID: 1nl3
TitleCRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM MYCOBACTERIUM TUBERCULOSIS in APO FORM
ComponentsPREPROTEIN TRANSLOCASE SECA 1 SUBUNIT
KeywordsPROTEIN TRANSPORT / PREPROTEIN TRANSLOCATION / ATPASE / TRANSMEMBRANE TRANSPORT / HELICASE-LIKE MOTOR DOMAIN / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


Tolerance of reactive oxygen produced by macrophages / cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting / peptidoglycan-based cell wall / ATP hydrolysis activity ...Tolerance of reactive oxygen produced by macrophages / cell envelope Sec protein transport complex / protein-exporting ATPase activity / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting / peptidoglycan-based cell wall / ATP hydrolysis activity / extracellular region / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SecA P-loop domain / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain ...Pre-protein croslinking domain of SecA / SecA, preprotein cross-linking domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SecA P-loop domain / SecA, C-terminal helicase domain / 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 / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein translocase subunit SecA 1 / Protein translocase subunit SecA 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSharma, V. / Arockiasamy, A. / Ronning, D.R. / Savva, C.G. / Holzenburg, A. / Braunstein, M. / Jacobs Jr., W.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of M. tuberculosis SecA, A Preprotein Translocating ATPase
Authors: Sharma, V. / Arockiasamy, A. / Ronning, D.R. / Savva, C.G. / Holzenburg, A. / Braunstein, M. / Jacobs Jr., W.R. / Sacchettini, J.C.
History
DepositionJan 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT
B: PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)206,9282
Polymers206,9282
Non-polymers00
Water16,754930
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-21 kcal/mol
Surface area74690 Å2
MethodPISA
2
A: PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT
B: PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT

A: PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT
B: PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)413,8564
Polymers413,8564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area13540 Å2
ΔGint-89 kcal/mol
Surface area141230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.196, 206.196, 295.412
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsThe biological assembly is probably the dimer in the asymmetric unit

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Components

#1: Protein PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT


Mass: 103463.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: SECA1 OR SECA OR RV3240C / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A5Y8, UniProt: P9WGP5*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 930 / 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: 4.38 Å3/Da / Density % sol: 71.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris.HCl, sodium formate, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris-HCl1reservoirpH7.5
23.5-3.7 Msodium formate1reservoir
35-10 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 22, 2002
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.75→100 Å / Num. all: 95337 / Num. obs: 95337 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.096
Reflection shellResolution: 2.75→2.85 Å / Rsym value: 0.461 / % possible all: 91.9
Reflection
*PLUS
Lowest resolution: 100 Å / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 91.9 % / Num. unique obs: 8700 / Rmerge(I) obs: 0.461

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→8 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.615 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.413 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25884 4386 5.1 %RANDOM
Rwork0.19254 ---
obs0.19587 82072 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.355 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.51 Å20 Å2
2--1.03 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13279 0 0 930 14209
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02113491
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.96418236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15351673
X-RAY DIFFRACTIONr_chiral_restr0.0970.22039
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210287
X-RAY DIFFRACTIONr_nbd_refined0.240.27370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2919
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.26
X-RAY DIFFRACTIONr_mcbond_it0.6671.58311
X-RAY DIFFRACTIONr_mcangle_it1.291213324
X-RAY DIFFRACTIONr_scbond_it1.62135180
X-RAY DIFFRACTIONr_scangle_it2.894.54912
LS refinement shellResolution: 2.8→2.864 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.368 287
Rwork0.319 5380
obs-5380
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.43

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