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- PDB-4b4a: Structure of the TatC core of the twin arginine protein transloca... -

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Entry
Database: PDB / ID: 4b4a
TitleStructure of the TatC core of the twin arginine protein translocation system
ComponentsSEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATC
KeywordsTRANSPORT PROTEIN / TAT SECRETION SYSTEM / PROTEIN TRANSLOCATION
Function / homologySec-independent periplasmic protein translocase TatC / Sec-independent periplasmic protein translocase, conserved site / Sec-independent protein translocase protein (TatC) / TatC family signature. / proton motive force dependent protein transmembrane transporter activity / TAT protein transport complex / protein transport by the Tat complex / intracellular protein transmembrane transport / Sec-independent protein translocase protein TatC
Function and homology information
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsRollauer, S.E. / Tarry, M.J. / Jaaskelainen, M. / Graham, J.E. / Jaeger, F. / Krehenbrink, M. / Roversi, P. / McDowell, M.A. / Stansfeld, P.J. / Johnson, S. ...Rollauer, S.E. / Tarry, M.J. / Jaaskelainen, M. / Graham, J.E. / Jaeger, F. / Krehenbrink, M. / Roversi, P. / McDowell, M.A. / Stansfeld, P.J. / Johnson, S. / Liu, S.M. / Lukey, M.J. / Marcoux, J. / Robinson, C.V. / Sansom, M.S. / Palmer, T. / Hogbom, M. / Berks, B.C. / Lea, S.M.
CitationJournal: Nature / Year: 2012
Title: Structure of the Tatc Core of the Twin-Arginine Protein Transport System.
Authors: Rollauer, S.E. / Tarry, M.J. / Graham, J.E. / Jaaskelainen, M. / Jager, F. / Johnson, S. / Krehenbrink, M. / Liu, S. / Lukey, M.J. / Marcoux, J. / Mcdowell, M.A. / Rodriguez, F. / Roversi, P. ...Authors: Rollauer, S.E. / Tarry, M.J. / Graham, J.E. / Jaaskelainen, M. / Jager, F. / Johnson, S. / Krehenbrink, M. / Liu, S. / Lukey, M.J. / Marcoux, J. / Mcdowell, M.A. / Rodriguez, F. / Roversi, P. / Stansfeld, P.J. / Robinson, C.V. / Sansom, M.S.P. / Palmer, T. / Hogbom, M. / Berks, B.C. / Lea, S.M.
History
DepositionJul 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4282
Polymers28,4231
Non-polymers1,0051
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.520, 123.520, 216.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein SEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATC / TATC


Mass: 28422.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ONE MOLECULE OF DETERGENT LMNG BOUND AT CRYSTALLOGRAPHIC 2-FOLD
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): LEMO56DE3 / References: UniProt: O67305
#2: Chemical ChemComp-LMN / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside


Mass: 1005.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H88O22 / Comment: detergent*YM
Sequence detailsC-TERMINAL ADDITIONAL TAG FROM VECTOR OF PGSENLYFQ FOLLOWING FULL TATC SEQUENCE

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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: 5.59 Å3/Da / Density % sol: 0.78 % / Description: NONE
Crystal growpH: 4
Details: 0.2M AMMONIUM SULPHATE, 0.02M NACL, 0.02M SODIUM ACETATE PH4.0, 33% V/V PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.5→15 Å / Num. obs: 7820 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 132.26 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.9
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.4 / % possible all: 96.6

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Processing

Software
NameVersionClassification
XDSTHROUGH XIA2data reduction
AimlessTHROUGH XIA2data scaling
PHENIX.HYSSphasing
autoSHARPphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.5→22 Å / Cor.coef. Fo:Fc: 0.8869 / Cor.coef. Fo:Fc free: 0.8553 / SU R Cruickshank DPI: 4.314 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.44 / SU Rfree Blow DPI: 0.479 / SU Rfree Cruickshank DPI: 0.497
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2882 386 4.89 %RANDOM
Rwork0.2518 ---
obs0.2535 7900 96.29 %-
Displacement parametersBiso mean: 159.38 Å2
Baniso -1Baniso -2Baniso -3
1--18.3276 Å20 Å20 Å2
2---18.3276 Å20 Å2
3---36.6553 Å2
Refine analyzeLuzzati coordinate error obs: 0.92 Å
Refinement stepCycle: LAST / Resolution: 3.5→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 69 0 1873
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012007HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.272808HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d670SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes19HARMONIC2
X-RAY DIFFRACTIONt_gen_planes266HARMONIC5
X-RAY DIFFRACTIONt_it2007HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion24.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion267SEMIHARMONIC5
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_contact2308SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2484 126 5.78 %
Rwork0.2399 2053 -
all0.2404 2179 -
obs--96.29 %

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