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- PDB-4htt: Crystal Structure of Twin Arginine Translocase Receptor- TatC in DDM -

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Basic information

Entry
Database: PDB / ID: 4htt
TitleCrystal Structure of Twin Arginine Translocase Receptor- TatC in DDM
ComponentsSec-independent protein translocase protein TatC, Lysozyme
KeywordsHYDROLASE / Twin arginine translocase receptor / Membrane
Function / homology
Function and homology information


proton motive force dependent protein transmembrane transporter activity / TAT protein transport complex / protein transport by the Tat complex / intracellular protein transmembrane transport / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Sec-independent periplasmic protein translocase TatC / Sec-independent periplasmic protein translocase, conserved site / Sec-independent protein translocase protein (TatC) / TatC family signature. / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Sec-independent protein translocase protein TatC / Endolysin
Similarity search - Component
Biological speciesAquifex aeolicus VF5 (bacteria)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 6.8 Å
AuthorsRamasamy, S. / Suloway, C.J.M. / Clemons Jr., W.M.
CitationJournal: Structure / Year: 2013
Title: The Glove-like Structure of the Conserved Membrane Protein TatC Provides Insight into Signal Sequence Recognition in Twin-Arginine Translocation.
Authors: Ramasamy, S. / Abrol, R. / Suloway, C.J. / Clemons, W.M.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

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Assembly

Deposited unit
A: Sec-independent protein translocase protein TatC, Lysozyme
B: Sec-independent protein translocase protein TatC, Lysozyme


Theoretical massNumber of molelcules
Total (without water)94,6902
Polymers94,6902
Non-polymers00
Water00
1
A: Sec-independent protein translocase protein TatC, Lysozyme


Theoretical massNumber of molelcules
Total (without water)47,3451
Polymers47,3451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sec-independent protein translocase protein TatC, Lysozyme


Theoretical massNumber of molelcules
Total (without water)47,3451
Polymers47,3451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.015, 142.015, 251.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Sec-independent protein translocase protein TatC, Lysozyme / Endolysin / Lysis protein / Muramidase


Mass: 47344.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: VF5 / Gene: tatC, aq_1267, E / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21) / References: UniProt: O67305, UniProt: P00720, lysozyme
Sequence detailsAUTHOR STATES THAT THIS PROTEIN WAS SET UP AS A FUSION THAT CRYSTALLIZED IN A UNIQUE SPACE GROUP. ...AUTHOR STATES THAT THIS PROTEIN WAS SET UP AS A FUSION THAT CRYSTALLIZED IN A UNIQUE SPACE GROUP. T4 LYSOZYME WAS VERIFIED IN THE CONSTRUCT AND IN THE DROP AND DATA WAS COLLECTED IN 2008. WHEN THEY SOLVED THE STRUCTURE BY MOLECULAR REPLACEMENT RECENTLY THEY WERE SURPRISED THAT THEY COULDN'T FIND THE LYSOZYME IN THE DENSITY AND FELT THEY COULDN'T INTERPRET ANYTHING WITH CONFIDENCE. SO, IN THE END THEY DON NOT HAVE ANY OF THE T4 LYSOZYME PART IN THE MODEL.

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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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 35% (v/v) PEG 400, ADA pH 6.6 and 0.1 M Potassium phosphate monobasic., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.08 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 6.8→125.874 Å / Num. all: 2281 / Num. obs: 2281 / % possible obs: 95.9 % / Observed criterion σ(F): 40.25 / Observed criterion σ(I): 8.37 / Redundancy: 6.8 % / Rsym value: 0.048 / Net I/σ(I): 22.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
6.8-7.1770.790.922863260.7996.9
7.17-7.670.4381.621763110.43896.4
7.6-8.136.90.2592.919922870.25996.6
8.13-8.786.90.1285.818642710.12897.2
8.78-9.626.80.07110.317522570.07196.6
9.62-10.756.90.05213.116052340.05296.2
10.75-12.426.60.03716.513482040.03795.6
12.42-15.216.50.02921.211471770.02996.3
15.21-21.56.30.02520.58981430.02596
21.5-39.255.50.02617.8390710.02677.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
SCALA3.3.20data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.8→30 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 3.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.4182 98 4.1 %RANDOM
Rwork0.3437 ---
all0.3437 2385 --
obs0.3437 2262 95.2 %-
Solvent computationBsol: 373.009 Å2
Displacement parametersBiso max: 731.91 Å2 / Biso mean: 474.4706 Å2 / Biso min: 207.69 Å2
Baniso -1Baniso -2Baniso -3
1-67.644 Å20 Å20 Å2
2--67.644 Å20 Å2
3----135.289 Å2
Refinement stepCycle: LAST / Resolution: 6.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 0 0 3608
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d0.931
X-RAY DIFFRACTIONc_mcbond_it18.07815
X-RAY DIFFRACTIONc_scbond_it17.91220
X-RAY DIFFRACTIONc_mcangle_it28.02820
X-RAY DIFFRACTIONc_scangle_it26.35625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
6.8-7.040.336170.389821121896
7.04-7.320.427990.356521522495.7
7.32-7.650.608100.344420921995.2
7.65-8.040.3797110.310521923095.8
8.04-8.530.3411110.281820721896
8.53-9.180.286970.217521822595.3
9.18-10.070.3012100.235921622695
10.07-11.450.575770.309521221994
11.45-14.170.3048140.356122423895.2
14.17-300.5568120.437123324593.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top

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