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Basic information

Entry
Database: PDB / ID: 2ibm
TitleA novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA
ComponentsPreprotein translocase secA subunit
KeywordsPROTEIN TRANSPORT / protein translocation / SecA / signal peptide binding
Function / homology
Function and homology information


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 / membrane raft / ATP binding / metal ion binding ...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 / membrane raft / ATP binding / metal ion binding / plasma membrane / 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 / SEC-C motif / SEC-C motif / SecA, C-terminal helicase domain / Protein translocase subunit SecA / SecA DEAD-like, N-terminal ...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 / SEC-C motif / SEC-C motif / 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
ADENOSINE-5'-DIPHOSPHATE / Protein translocase subunit SecA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZimmer, J. / Li, W. / Rapoport, T.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: A Novel Dimer Interface and Conformational Changes Revealed by an X-ray Structure of B. subtilis SecA.
Authors: Zimmer, J. / Li, W. / Rapoport, T.A.
History
DepositionSep 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 subunit
B: Preprotein translocase secA subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,2603
Polymers177,8322
Non-polymers4271
Water0
1
A: Preprotein translocase secA subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3432
Polymers88,9161
Non-polymers4271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Preprotein translocase secA subunit


Theoretical massNumber of molelcules
Total (without water)88,9161
Polymers88,9161
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Preprotein translocase secA subunit
B: Preprotein translocase secA subunit
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)356,5196
Polymers355,6654
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area24710 Å2
ΔGint-56 kcal/mol
Surface area122070 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)125.834, 166.833, 211.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThe asymmetric unit contains two copies of the molecule. The monomer is believed to be the biologically active species.

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Components

#1: Protein Preprotein translocase secA subunit


Mass: 88916.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: secA, div+ / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P28366
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 301 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.8 M malonate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 301K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 19-ID11.1
SYNCHROTRONNSLS X2520.98
Detector
TypeIDDetectorDateDetails
SBC-21CCDMay 1, 2005mirrors
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.981
ReflectionResolution: 3.2→100 Å / Num. obs: 39088 / % possible obs: 92.7 % / Observed criterion σ(F): 7 / Observed criterion σ(I): 2.7 / Redundancy: 4.5 % / Rsym value: 0.066 / Net I/σ(I): 5.8
Reflection shellHighest resolution: 3.2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.571 / % possible all: 92.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1m6n

1m6n


Resolution: 3.2→40.53 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 55688.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.323 3431 10 %RANDOM
Rwork0.321 ---
obs0.321 34442 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.0038 Å2 / ksol: 0.38555 e/Å3
Displacement parametersBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å20 Å2
2--4.57 Å20 Å2
3----2.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.2→40.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12376 0 27 0 12403
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.651.5
X-RAY DIFFRACTIONc_mcangle_it4.212
X-RAY DIFFRACTIONc_scbond_it1.362
X-RAY DIFFRACTIONc_scangle_it1.972.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 506 9.7 %
Rwork0.394 4719 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2adp_cns.paradp_cns.top
X-RAY DIFFRACTION3ion.paramion.top

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