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- PDB-5k94: Deletion-Insertion Chimera of MBP with the Preprotein Cross-Linki... -

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Basic information

Entry
Database: PDB / ID: 5k94
TitleDeletion-Insertion Chimera of MBP with the Preprotein Cross-Linking Domain of the SecA ATPase
ComponentsMaltose-binding periplasmic protein,Protein translocase subunit SecA,Maltose-binding periplasmic protein
KeywordsPROTEIN TRANSPORT / preprotein translocase / SecA / preprotein cross-linking domain / PPXD / MBP chimera
Function / homology
Function and homology information


protein-secreting ATPase / intracellular protein transmembrane transport / protein import / carbohydrate transmembrane transporter activity / protein targeting / outer membrane-bounded periplasmic space / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
SEC-C motif / SEC-C motif / 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 ...SEC-C motif / SEC-C motif / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Protein translocase subunit SecA
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShilton, B.H. / Hackett, J. / Ghonaim, N.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)217494 Canada
CitationJournal: FEBS Lett. / Year: 2017
Title: Characterization of a polypeptide-binding site in the DEAD Motor of the SecA ATPase.
Authors: Khalili Yazdi, A. / Namjoshi, S. / Hackett, J. / Ghonaim, N. / Shilton, B.H.
History
DepositionMay 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Protein translocase subunit SecA,Maltose-binding periplasmic protein
B: Maltose-binding periplasmic protein,Protein translocase subunit SecA,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4184
Polymers112,8532
Non-polymers5652
Water8,179454
1
A: Maltose-binding periplasmic protein,Protein translocase subunit SecA,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7092
Polymers56,4271
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein,Protein translocase subunit SecA,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7092
Polymers56,4271
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.880, 165.260, 43.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Maltose-binding periplasmic protein,Protein translocase subunit SecA,Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein


Mass: 56426.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: malE, Z5632, ECs5017, secA, Z0108, ECs0102 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEY0, UniProt: Q8X996
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM PCB buffer (Qiagen; sodium propionate, sodium cacodylate, bis-tris propane), pH 7.0; 19.5 % PEG 1500; 10% glycerol; 28 mg/mL protein concentration

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→45.2 Å / Num. obs: 110536 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 34.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.89
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.150.3812.38174.9
2.15-2.210.3223.03180.4
2.21-2.280.2733.83191.1
2.28-2.350.2394.93197.2
2.35-2.420.2236.37199.9
2.42-2.510.1867.9199.8
2.51-2.60.1589.38199.9
2.6-2.710.1311.43199.9
2.71-2.830.10713.711100
2.83-2.970.08915.921100
2.97-3.130.07518.441100
3.13-3.320.06321.62199.9
3.32-3.550.05225.07199.9
3.55-3.830.04527.91199.9
3.83-4.20.0430.2199.8
4.2-4.70.03931.571100
4.7-5.420.03831.77199.9
5.42-6.640.03531.891100
6.64-9.390.02934.16199.9
9.390.02633.91197.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMP

1omp


Resolution: 2.1→17.965 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 23.82
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 2991 5.11 %Random Selection
Rwork0.202 ---
obs0.2034 58556 96.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.8 Å2 / Biso mean: 49.6661 Å2 / Biso min: 18.1 Å2
Refinement stepCycle: final / Resolution: 2.1→17.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7936 0 38 454 8428
Biso mean--82.47 44.02 -
Num. residues----1012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028144
X-RAY DIFFRACTIONf_angle_d0.52111030
X-RAY DIFFRACTIONf_chiral_restr0.041200
X-RAY DIFFRACTIONf_plane_restr0.0031432
X-RAY DIFFRACTIONf_dihedral_angle_d12.7414902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13440.38411160.28122027214376
2.1344-2.17110.31481100.26832201231180
2.1711-2.21050.29031110.26192223233483
2.2105-2.2530.28651560.25112376253289
2.253-2.29890.31211400.24972613275395
2.2989-2.34880.28791580.24492664282299
2.3488-2.40330.32721480.237826982846100
2.4033-2.46320.27341410.234927442885100
2.4632-2.52960.27741250.227627042829100
2.5296-2.60390.24761530.22527512904100
2.6039-2.68760.27291450.225726922837100
2.6876-2.78340.23611490.216427422891100
2.7834-2.89440.28081480.222927552903100
2.8944-3.02550.26041340.220427192853100
3.0255-3.18420.26881640.224627432907100
3.1842-3.38250.2361290.212527952924100
3.3825-3.64160.21911490.19327632912100
3.6416-4.00440.19981460.175527802926100
4.0044-4.57550.19761570.163127752932100
4.5755-5.73330.17281570.17528362993100
5.7333-17.96530.17381550.175929643119100
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)
11.7348-1.73050.50985.8062-2.67034.214-0.0296-0.0630.11330.36290.11920.1883-0.5941-0.433-0.06680.27890.0550.05490.2592-0.08710.194-37.289613.480928.6337
27.2363-0.9639-1.37965.94561.19024.4238-0.4685-0.245-0.58920.26050.53820.66730.6697-0.2456-0.09260.2958-0.01960.04020.29850.14640.5189-5.345615.630111.3669
31.2229-0.88920.62974.7074-2.17233.16350.0450.0088-0.06490.3582-0.0877-0.0711-0.4078-0.12590.03440.26990.06310.0450.2365-0.06410.2271-32.81236.1731.9191
43.71611.74-2.08541.7875-1.11733.90780.1522-0.25020.08970.0314-0.08980.069-0.5491-0.0206-0.03820.3070.0572-0.07910.2561-0.08120.2497-16.425855.2125-6.1598
50.15130.23870.20455.0806-2.20051.6464-0.00820.08180.12750.2224-0.0034-0.1215-0.25130.32570.02490.1982-0.0397-0.0530.39120.02180.40429.846237.01919.2186
63.80051.0589-1.85641.5049-0.8092.97080.1909-0.10240.1441-0.0252-0.0718-0.0679-0.63990.1317-0.0980.3669-0.0831-0.02690.2539-0.05490.2096-10.158558.9004-10.1562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 231 )A1 - 231
2X-RAY DIFFRACTION2chain 'A' and (resid 232 through 361 )A232 - 361
3X-RAY DIFFRACTION3chain 'A' and (resid 362 through 1370 )A362 - 1370
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 163 )B1 - 163
5X-RAY DIFFRACTION5chain 'B' and (resid 164 through 1200 )B164 - 1200
6X-RAY DIFFRACTION6chain 'B' and (resid 1201 through 1370 )B0

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