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- PDB-4r2l: Crystal structure of YnaF (Universal Stress Protein F) from Salmo... -

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Basic information

Entry
Database: PDB / ID: 4r2l
TitleCrystal structure of YnaF (Universal Stress Protein F) from Salmonella typhimurium
ComponentsUniversal stress protein F
KeywordsUNKNOWN FUNCTION / Universal stress protein / HUP domain / Stress tolerance / ATP binding / Chloride binding
Function / homology
Function and homology information


Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Universal stress protein F
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBangera, M. / Murthy, M.R.N.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural and functional analysis of two universal stress proteins YdaA and YnaF from Salmonella typhimurium: possible roles in microbial stress tolerance.
Authors: Bangera, M. / Panigrahi, R. / Sagurthi, S.R. / Savithri, H.S. / Murthy, M.R.
History
DepositionAug 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Universal stress protein F
B: Universal stress protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,00611
Polymers34,6862
Non-polymers1,3209
Water3,603200
1
A: Universal stress protein F
B: Universal stress protein F
hetero molecules

A: Universal stress protein F
B: Universal stress protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,01222
Polymers69,3724
Non-polymers2,64018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area14700 Å2
ΔGint-130 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.760, 132.760, 32.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-342-

HOH

21B-415-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Universal stress protein F


Mass: 17343.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / Gene: STM1652, uspF, ynaF uspF STM1652 / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P67091

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Non-polymers , 5 types, 209 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 298 K / Method: under oil, microbatch / pH: 8.5
Details: 30% PEG 4000, 100mM Tris-HCl pH 8.5, 200mM Magnesium chloride, 100mM guanidine hydrochloride, Under oil, Microbatch, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2011 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.8→33.19 Å / Num. obs: 27850 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.075
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3980 / Rsym value: 0.675 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBE2data collection
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3FH0

3fh0


Resolution: 1.8→33.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.265 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23471 1397 5 %RANDOM
Rwork0.18913 ---
obs0.19133 26406 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.983 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å20 Å2
2---0.43 Å2-0 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 78 200 2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192215
X-RAY DIFFRACTIONr_bond_other_d0.0020.022145
X-RAY DIFFRACTIONr_angle_refined_deg1.9152.023038
X-RAY DIFFRACTIONr_angle_other_deg0.92734944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7624.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61915362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7331510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212409
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_mcbond_it1.3661.5531124
X-RAY DIFFRACTIONr_mcbond_other1.3661.5531123
X-RAY DIFFRACTIONr_mcangle_it2.2632.3171402
X-RAY DIFFRACTIONr_mcangle_other2.2632.3161403
X-RAY DIFFRACTIONr_scbond_it1.731.7421091
X-RAY DIFFRACTIONr_scbond_other1.7291.7421091
X-RAY DIFFRACTIONr_scangle_other2.6492.5541629
X-RAY DIFFRACTIONr_long_range_B_refined6.83414.2852588
X-RAY DIFFRACTIONr_long_range_B_other6.83314.2942589
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 106 -
Rwork0.264 1897 -
obs--99.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.5505-2.24190.82693.28280.41772.33550.0346-0.22840.3432-0.2337-0.11350.3752-0.0825-0.37170.07890.04270.0555-0.00430.1802-0.00550.190219.078-39.332-6.826
23.6036-0.181-0.77875.2995-0.02042.87840.1620.059-0.2725-0.159-0.0988-0.27990.3074-0.0518-0.06320.07320.0132-0.00180.01210.01490.059638.499-58.8-11.515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 144
2X-RAY DIFFRACTION2B2 - 144

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