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- PDB-4ryu: Crystal Structure of C2 form of E112A Mutant of Stationary Phase ... -

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Basic information

Entry
Database: PDB / ID: 4ryu
TitleCrystal Structure of C2 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 enterica subsp. enterica serovar Enteritidis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 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 / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.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_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_asym_id / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,04525
Polymers114,2284
Non-polymers1,81621
Water16,808933
1
A: 5'/3'-nucleotidase SurE
B: 5'/3'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,17914
Polymers57,1142
Non-polymers1,06512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-155 kcal/mol
Surface area20610 Å2
MethodPISA
2
C: 5'/3'-nucleotidase SurE
D: 5'/3'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,86511
Polymers57,1142
Non-polymers7519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-142 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.390, 95.780, 94.230
Angle α, β, γ (deg.)90.00, 100.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 28557.074 Da / Num. of mol.: 4 / Mutation: E112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Enteritidis (bacteria)
Strain: EC20130345 / Gene: AV66_15865, surE / Plasmid: pRSETC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLysS
References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase

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Non-polymers , 5 types, 954 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 933 / 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: 3.12 Å3/Da / Density % sol: 60.57 %
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: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 11, 2012 / 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: 2.03→47.87 Å / Num. obs: 89024 / % possible obs: 98.6 % / Redundancy: 4 % / Biso Wilson estimate: 29.96 Å2 / Rsym value: 0.085 / Net I/σ(I): 11.5
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 11902 / Rsym value: 0.534 / % possible all: 91

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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: 2.04→48 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.738 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21415 4465 5 %RANDOM
Rwork0.17809 ---
obs0.17991 84553 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20.12 Å2
2--0.21 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.04→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7592 0 108 933 8633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.027988
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.97310972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98651065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63423.776339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.674151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0231561
X-RAY DIFFRACTIONr_chiral_restr0.0790.21273
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216173
LS refinement shellResolution: 2.04→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 299 -
Rwork0.351 5676 -
obs--92.52 %

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