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- PDB-2rjo: Crystal structure of Twin-arginine translocation pathway signal p... -

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Basic information

Entry
Database: PDB / ID: 2rjo
TitleCrystal structure of Twin-arginine translocation pathway signal protein from Burkholderia phytofirmans
ComponentsTwin-arginine translocation pathway signal protein
KeywordsSIGNALING PROTEIN / PSI-2 / NYSGXRC / twin arginine translocation pathway signal protein / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / : / Periplasmic binding protein/LacI transcriptional regulator
Similarity search - Component
Biological speciesBurkholderia phytofirmans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of twin-arginine translocation pathway signal protein from Burkholderia phytofirmans.
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / chem_comp / citation_author
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Twin-arginine translocation pathway signal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7446
Polymers36,1801
Non-polymers5645
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.197, 51.504, 138.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Twin-arginine translocation pathway signal protein


Mass: 36179.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phytofirmans (bacteria) / Strain: PsJN / Gene: BphytDRAFT_4841 / Plasmid: pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: A0GG20, UniProt: B2TEP5*PLUS
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 25% PEG 8000, 1% D-galactose, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2007 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 20727 / Num. obs: 20727 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.6
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 1 / Num. unique all: 1039 / % possible all: 44.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→41.2 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 57664.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 560 2.9 %RANDOM
Rwork0.234 ---
obs0.234 19564 82.3 %-
all-20727 --
Solvent computationBsol: 38.5128 Å2 / ksol: 0.372992 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.92 Å20 Å20 Å2
2---6.58 Å20 Å2
3----4.34 Å2
Refine analyzeLuzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.05→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 32 119 2589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 52 2.7 %
Rwork0.322 1848 -
obs--49.2 %
Xplor file
Refine-IDSerial noTopol file
X-RAY DIFFRACTION1protein.top
X-RAY DIFFRACTION2gal.top

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