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- PDB-4ryt: Crystal Structure of F222 form of E112A Mutant of Stationary Phas... -

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Basic information

Entry
Database: PDB / ID: 4ryt
TitleCrystal Structure of F222 form of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium
Components5'/3'-nucleotidase SurE
KeywordsHYDROLASE / Stationary phase survival protein / Domain swapping / Rossmann fold like / Phosphatase
Function / homology
Function and homology information


3'-nucleotidase / exopolyphosphatase / 3'-nucleotidase activity / exopolyphosphatase activity / : / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Stationary-phase Survival Protein Sure Homolog; Chain: A, / Survival protein SurE-like phosphatase/nucleotidase / Survival protein SurE / Survival protein SurE-like phosphatase/nucleotidase / SurE-like phosphatase/nucleotidase superfamily / Survival protein SurE / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 5'/3'-nucleotidase SurE
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsMathiharan, Y.K. / Murthy, M.R.N.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Insights into stabilizing interactions in the distorted domain-swapped dimer of Salmonella typhimurium survival protein.
Authors: Mathiharan, Y.K. / Savithri, H.S. / Murthy, M.R.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_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.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'/3'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0208
Polymers28,5571
Non-polymers4637
Water5,206289
1
A: 5'/3'-nucleotidase SurE
hetero molecules

A: 5'/3'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,03916
Polymers57,1142
Non-polymers92514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_545-x+1/2,-y-1/2,z1
Buried area10790 Å2
ΔGint-88 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.010, 121.180, 143.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

21A-439-

HOH

31A-456-

HOH

41A-463-

HOH

51A-501-

HOH

61A-610-

HOH

71A-623-

HOH

81A-676-

HOH

91A-684-

HOH

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Components

#1: Protein 5'/3'-nucleotidase SurE / Exopolyphosphatase / Nucleoside monophosphate phosphohydrolase


Mass: 28557.074 Da / Num. of mol.: 1 / Mutation: E112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: surE / Plasmid: pRSETC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLysS
References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M HEPES (pH 7.5), 30% 2-Methyl 2,4-pentanediol, Under Oil, Microbatch method, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 27, 2013 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.07→46.33 Å / Num. obs: 18453 / % possible obs: 94 % / Redundancy: 4.9 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.112 / Net I/σ(I): 12.6
Reflection shellResolution: 2.07→2.18 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 2258 / Rsym value: 0.197 / % possible all: 79.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2V4N

2v4n


Resolution: 2.09→36 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.391 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 941 5.1 %RANDOM
Rwork0.20343 ---
obs0.2055 17512 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.672 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å20 Å20 Å2
2---2.06 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.09→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 27 289 2188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022010
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9692770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9885278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26224.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09615283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1931512
X-RAY DIFFRACTIONr_chiral_restr0.0710.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211575
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 64 -
Rwork0.27 1199 -
obs--95.9 %

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