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

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Basic information

Entry
Database: PDB / ID: 1nkt
TitleCRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEX WITH ADPBS
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 / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site ...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 / 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, C-terminal helicase domain / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA P-loop 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Protein translocase subunit SecA 1 / Protein translocase subunit SecA 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.601 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 3, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,8316
Polymers206,9282
Non-polymers9034
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-57 kcal/mol
Surface area73180 Å2
MethodPISA
2
A: Preprotein translocase secA 1 subunit
B: Preprotein translocase secA 1 subunit
hetero molecules

A: Preprotein translocase secA 1 subunit
B: Preprotein translocase secA 1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,66212
Polymers413,8564
Non-polymers1,8068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area17900 Å2
ΔGint-168 kcal/mol
Surface area138140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.050, 206.050, 292.857
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 4.34 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris.HCl, sodium formate, glycerol, magnesium chloride, 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

Diffraction
IDMean temperature (K)Crystal-ID
11731
21731
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.0332
SYNCHROTRONAPS 14-BM-D20.9611, 0.9797, 0.98, 1.00348
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDJul 21, 2002
ADSC QUANTUM 42CCDDec 23, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double-crystalSINGLE WAVELENGTHMx-ray1
2Si(111) double-crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.96111
30.97971
40.981
51.003481
ReflectionResolution: 2.4→95.35 Å / Num. all: 139810 / Num. obs: 139810 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.089
Reflection shellResolution: 2.4→2.49 Å / Num. unique all: 13803 / Rsym value: 0.483 / % possible all: 98.2
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 100 Å / Num. obs: 13803 / Num. measured all: 139810 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.48 / Num. unique obs: 13803

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.601→95.35 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.616 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.298 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26498 5631 5.1 %RANDOM
Rwork0.21316 ---
obs0.21574 105541 99.01 %-
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: 18.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.601→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13260 0 56 546 13862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02113530
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.96918298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05151668
X-RAY DIFFRACTIONr_chiral_restr0.1120.22042
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210292
X-RAY DIFFRACTIONr_nbd_refined0.2340.26489
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2717
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.28
X-RAY DIFFRACTIONr_mcbond_it0.6541.58286
X-RAY DIFFRACTIONr_mcangle_it1.279213290
X-RAY DIFFRACTIONr_scbond_it2.10535244
X-RAY DIFFRACTIONr_scangle_it3.5334.55008
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.434 395
Rwork0.375 7128
obs-7128
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 99 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.56

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