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- PDB-3i45: CRYSTAL STRUCTURE OF putative twin-arginine translocation pathway... -

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Basic information

Entry
Database: PDB / ID: 3i45
TitleCRYSTAL STRUCTURE OF putative twin-arginine translocation pathway signal protein from Rhodospirillum rubrum Atcc 11170
ComponentsTwin-arginine translocation pathway signal protein
KeywordsSIGNALING PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / twin-arginine translocation pathway signal protein / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


amino acid transport
Similarity search - Function
Leu/Ile/Val-binding protein / Leucine-binding protein domain / Periplasmic binding protein / 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
NICOTINIC ACID / Twin-arginine translocation pathway signal
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å
AuthorsMalashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative twin-arginine translocation pathway signal protein from Rhodospirillum rubrum Atcc 11170
Authors: Malashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: 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 1.4Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)42,6922
Polymers42,5691
Non-polymers1231
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.473, 91.835, 48.166
Angle α, β, γ (deg.)90.000, 106.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Twin-arginine translocation pathway signal protein


Mass: 42569.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Strain: ATCC 11170 / Gene: Rru_A0563 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q2RWX8
#2: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 8000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 2.1 % / Av σ(I) over netI: 27.46 / Number: 321373 / Rmerge(I) obs: 0.039 / Χ2: 1.6 / D res high: 1.36 Å / D res low: 50 Å / Num. obs: 156188 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.695092.910.0272.2482.1
2.933.6998.810.0251.9482
2.562.9399.410.0352.6452.1
2.332.5699.510.0453.2142.1
2.162.3399.410.0422.5872.1
2.032.1699.510.0411.9652.1
1.932.0399.510.0451.7332.1
1.851.9399.610.0531.5952.1
1.771.8599.610.0611.52.1
1.711.7799.610.0711.42.1
1.661.7199.610.0831.3032.1
1.611.6699.610.0971.2392.1
1.571.6199.610.1081.2152.1
1.531.5799.610.1281.1892
1.51.5399.610.1511.1172
1.471.599.610.1671.0642
1.441.4799.610.2041.0262
1.411.4499.810.2350.9972
1.381.4199.710.2750.9752
1.361.3898.810.3090.9112
ReflectionResolution: 1.36→50 Å / Num. obs: 156188 / % possible obs: 99.2 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.039 / Χ2: 1.603 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.36-1.3820.30977710.911198.8
1.38-1.4120.27578350.975199.7
1.41-1.4420.23578720.997199.8
1.44-1.4720.20478711.026199.6
1.47-1.520.16778481.064199.6
1.5-1.5320.15178191.117199.6
1.53-1.5720.12877931.189199.6
1.57-1.612.10.10878541.215199.6
1.61-1.662.10.09778481.239199.6
1.66-1.712.10.08379131.303199.6
1.71-1.772.10.07178211.4199.6
1.77-1.852.10.06178551.5199.6
1.85-1.932.10.05378381.595199.6
1.93-2.032.10.04578201.733199.5
2.03-2.162.10.04178341.965199.5
2.16-2.332.10.04278312.587199.4
2.33-2.562.10.04578563.214199.5
2.56-2.932.10.03577912.645199.4
2.93-3.6920.02578241.948198.8
3.69-502.10.02772942.248192.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.36→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.934 / SU B: 1.723 / SU ML: 0.029 / SU R Cruickshank DPI: 0.011 / SU Rfree: 0.011 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.011 / ESU R Free: 0.011 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.174 3983 5 %RANDOM
Rwork0.158 ---
obs0.159 79310 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 46.46 Å2 / Biso mean: 12.741 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.04 Å2
2---0.12 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.36→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 9 436 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223061
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9624178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15223.015136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16915476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.891525
X-RAY DIFFRACTIONr_chiral_restr0.0820.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212391
X-RAY DIFFRACTIONr_mcbond_it0.6443.51902
X-RAY DIFFRACTIONr_mcangle_it1.837503049
X-RAY DIFFRACTIONr_scbond_it3.628501159
X-RAY DIFFRACTIONr_scangle_it1.0164.51122
LS refinement shellResolution: 1.357→1.393 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 275 -
Rwork0.199 5341 -
all-5616 -
obs--96.16 %
Refinement TLS params.Method: refined / Origin x: 3.1358 Å / Origin y: 4.5184 Å / Origin z: 35.1779 Å
111213212223313233
T0.0432 Å20.0037 Å2-0.0103 Å2-0.003 Å2-0.0054 Å2--0.0198 Å2
L0.7507 °20.1415 °2-0.1322 °2-0.2856 °2-0.0757 °2--0.8452 °2
S0.0069 Å °-0.0042 Å °-0.039 Å °0.0038 Å °0.0006 Å °0.0226 Å °0.0579 Å °-0.0179 Å °-0.0075 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 379
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A388 - 824

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