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- PDB-4r2m: Crystal Structure of R134D mutant of YnaF (Universal Stress Prote... -

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Basic information

Entry
Database: PDB / ID: 4r2m
TitleCrystal Structure of R134D mutant 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Universal stress protein F
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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.pdbx_ptnr2_label_alt_id / _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)35,6636
Polymers34,6022
Non-polymers1,0614
Water1,44180
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)71,32612
Polymers69,2044
Non-polymers2,1228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12760 Å2
ΔGint-84 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.180, 131.180, 33.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Universal stress protein F


Mass: 17300.945 Da / Num. of mol.: 2 / Mutation: R134D
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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 298 K / Method: under oil, microbatch / pH: 8.5
Details: 30% PEG 4000, 100mM Tris-HCl pH 8.5, 200mM Magnesium chloride, 5mM Adenosine 5'-(beta,gamma-imido)triphosphate, Under oil, Microbatch, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978565 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2014 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.2→41.48 Å / Num. obs: 15273 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.12
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2167 / Rsym value: 0.676 / % possible all: 100

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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 4R2L

4r2l


Resolution: 2.2→41.48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.425 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23435 765 5 %RANDOM
Rwork0.19532 ---
obs0.19728 14470 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.254 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å20 Å2
2---0.29 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 64 80 2218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192257
X-RAY DIFFRACTIONr_bond_other_d0.0010.022125
X-RAY DIFFRACTIONr_angle_refined_deg1.8142.0493111
X-RAY DIFFRACTIONr_angle_other_deg0.80634888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33324.78369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27215344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.72157
X-RAY DIFFRACTIONr_chiral_restr0.0790.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
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_it1.4122.3411134
X-RAY DIFFRACTIONr_mcbond_other1.4112.3411134
X-RAY DIFFRACTIONr_mcangle_it2.2763.5091415
X-RAY DIFFRACTIONr_mcangle_other2.2763.5081416
X-RAY DIFFRACTIONr_scbond_it1.7012.5261121
X-RAY DIFFRACTIONr_scbond_other1.7012.5251122
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6173.741695
X-RAY DIFFRACTIONr_long_range_B_refined5.62920.0062526
X-RAY DIFFRACTIONr_long_range_B_other5.55519.8052499
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 53 -
Rwork0.226 1043 -
obs--100 %
Refinement TLS params.

S22: -0.0158 Å ° / 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 °)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)
14.23410.08830.70644.64640.25983.01890.01670.06210.4498-0.0231-0.2516-0.18550.1576-0.00090.0716-0.0055-0.00580.00880.00370.0908-26.927-7.4183.211
24.74621.04780.17334.96780.38161.69030.0263-0.0944-0.06210.03080.63490.0399-0.2097-0.01050.02310.0019-0.00130.07510.0050.14-47.086-27.299-1.803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 144
2X-RAY DIFFRACTION2B3 - 144

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