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- PDB-4ew7: The crystal structure of conjugative transfer PAS_like domain fro... -

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Basic information

Entry
Database: PDB / ID: 4ew7
TitleThe crystal structure of conjugative transfer PAS_like domain from Salmonella enterica subsp. enterica serovar Typhimurium
ComponentsConjugative transfer: regulation
KeywordsTRANSCRIPTION / alpha-beta-alpha structure / Structural Genomics / Midwest Center for Structural Genomics (MCSG) / PSI-Biology / PAS-like fold / cytoplasmic / Program for the Characterization of Secreted Effector Proteins / PCSEP
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
Plasmid transfer regulator TraJ, R1 plasmid / PAS domain / Beta-Lactamase / PAS fold / PAS fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / PYRUVIC ACID / SUCCINIC ACID / Conjugative transfer: regulation / Conjugative transfer: regulation
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.67 Å
AuthorsWu, R. / Jedrzejczak, R.P. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
CitationJournal: To be Published
Title: The crystal structure of conjugative transfer PAS_like domain from Salmonella enterica subsp. enterica serovar Typhimurium
Authors: Wu, R. / Jedrzejczak, R.P. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Adkins, J.N. / Joachimiak, A.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conjugative transfer: regulation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1897
Polymers14,7721
Non-polymers4176
Water75742
1
A: Conjugative transfer: regulation
hetero molecules

A: Conjugative transfer: regulation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,37814
Polymers29,5452
Non-polymers83312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area3600 Å2
ΔGint-34 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.081, 57.081, 67.638
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Conjugative transfer: regulation


Mass: 14772.407 Da / Num. of mol.: 1
Fragment: conjugative transfer PAS_like domain residues 5-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Strain: 588858 / Gene: STM14_5595, traJ / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 MAGIC / References: UniProt: D0ZHW1, UniProt: A0A0F6AW83*PLUS

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Non-polymers , 7 types, 48 molecules

#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M DL, malic acid, pH 7.0, 20% PEG 3500, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2010 / Details: mirrors
RadiationMonochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 15181 / Num. obs: 15181 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 26.97 Å2 / Rsym value: 0.049 / Net I/σ(I): 14.9
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 659 / Rsym value: 0.452 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.67→27.912 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 17.68 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2278 760 5.02 %
Rwork0.1949 --
obs0.1965 15152 99.44 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.573 Å2 / ksol: 0.408 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4536 Å2-0 Å20 Å2
2---1.4536 Å2-0 Å2
3---2.9071 Å2
Refinement stepCycle: LAST / Resolution: 1.67→27.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 26 42 992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006981
X-RAY DIFFRACTIONf_angle_d0.9761324
X-RAY DIFFRACTIONf_dihedral_angle_d14.069362
X-RAY DIFFRACTIONf_chiral_restr0.078138
X-RAY DIFFRACTIONf_plane_restr0.004177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.67-1.79890.23871570.241828302987100
1.7989-1.97990.22921740.184628172991100
1.9799-2.26630.20591330.183529013034100
2.2663-2.85480.2281410.192829063047100
2.8548-27.9160.23141550.19592938309398
Refinement TLS params.Method: refined / Origin x: -5.8135 Å / Origin y: 40.0919 Å / Origin z: 16.4219 Å
111213212223313233
T0.1527 Å20.0703 Å20.0458 Å2-0.0535 Å20.0061 Å2--0.1017 Å2
L2.5962 °20.4634 °20.3624 °2-2.2109 °20.0955 °2--3.2271 °2
S-0.1945 Å °-0.3513 Å °-0.5627 Å °0.1044 Å °0.0623 Å °-0.2958 Å °0.6728 Å °0.2579 Å °0.0271 Å °
Refinement TLS groupSelection details: chain A

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