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- PDB-4iqn: Crystal structure of uncharacterized protein from Salmonella ente... -

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Basic information

Entry
Database: PDB / ID: 4iqn
TitleCrystal structure of uncharacterized protein from Salmonella enterica subsp. enterica serovar typhimurium str. 14028s
Components(Putative cytoplasmic ...) x 3
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / PROGRAM FOR THE CHARACTERIZATION OF SECRETED EFFECTOR PROTEINS / PCSEP / reductive METHYLATION
Function / homologyDomain of unknown function (DUF5066) / Protein of unknown function DUF5066 / Domain of unknown function (DUF5066) / SMI1/KNR4-like / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Putative cytoplasmic protein / Putative cytoplasmic protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsChang, C. / Hatzos-Skintges, C. / Adkins, J.N. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein from salmonella enterica subsp. enterica serovar typhimurium str. 14028s
Authors: Chang, C. / Hatzos-Skintges, C. / Adkins, J.N. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionJan 11, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJan 23, 2013ID: 4HG1
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytoplasmic protein
B: Putative cytoplasmic protein
C: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2845
Polymers78,9833
Non-polymers3002
Water9,836546
1
A: Putative cytoplasmic protein


Theoretical massNumber of molelcules
Total (without water)26,3051
Polymers26,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4662
Polymers26,3591
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5132
Polymers26,3181
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.138, 95.477, 69.897
Angle α, β, γ (deg.)90.00, 109.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Putative cytoplasmic ... , 3 types, 3 molecules ABC

#1: Protein Putative cytoplasmic protein


Mass: 26305.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028s / SGSC 2262 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D0ZRV8, UniProt: A0A0F6B4U8*PLUS
#2: Protein Putative cytoplasmic protein


Mass: 26359.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028s / SGSC 2262 / Production host: Escherichia coli (E. coli) / References: UniProt: D0ZRV8, UniProt: A0A0F6B4U8*PLUS
#3: Protein Putative cytoplasmic protein


Mass: 26318.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: 14028s / SGSC 2262 / Production host: Escherichia coli (E. coli) / References: UniProt: D0ZRV8, UniProt: A0A0F6B4U8*PLUS

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Non-polymers , 3 types, 548 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2012
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 79623 / Num. obs: 76983 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 41.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.71 / Num. unique all: 3773 / % possible all: 97.8

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Processing

Software
NameVersionClassification
SBC-CollectCOLLECTdata collection
MLPHAREphasing
DMmodel building
SHELXDEphasing
RESOLVEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→31.13 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.131 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19568 3848 5 %RANDOM
Rwork0.13496 ---
all0.13799 72717 --
obs0.13799 72717 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.887 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å2-0 Å2-1.44 Å2
2--2.96 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.75→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 20 546 5948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195819
X-RAY DIFFRACTIONr_bond_other_d0.0010.025419
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9957940
X-RAY DIFFRACTIONr_angle_other_deg0.839312536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.395723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70525.292308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46715905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8751538
X-RAY DIFFRACTIONr_chiral_restr0.0940.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216723
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021271
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr4.41311238
X-RAY DIFFRACTIONr_sphericity_free27.2575141
X-RAY DIFFRACTIONr_sphericity_bonded16.303511504
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 269 -
Rwork0.175 5052 -
obs-5229 93.14 %

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