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- PDB-4xj7: Crystal Structure of E112A Mutant of Stationary Phase Survival Pr... -

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Basic information

Entry
Database: PDB / ID: 4xj7
TitleCrystal Structure of E112A Mutant of Stationary Phase Survival Protein (SurE) from Salmonella typhimurium soaked with AMP
Components5'/3'-nucleotidase SurE
KeywordsHYDROLASE / Stationary phase survival protein / Domain swapping / Rossmann fold like / Phosphatase
Function / homology
Function and homology information


3'-nucleotidase / 3'-nucleotidase activity / exopolyphosphatase / exopolyphosphatase activity / XMP 5'-nucleosidase 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
ADENINE / ADENOSINE / PHOSPHATE ION / 5'/3'-nucleotidase SurE
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMathiharan, Y.K. / Murthy, M.R.N.
CitationJournal: Acta Crystallogr.,Sect.D / 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
DepositionJan 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
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_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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

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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)115,65118
Polymers114,2284
Non-polymers1,42314
Water24,9511385
1
A: 5'/3'-nucleotidase SurE
B: 5'/3'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,93910
Polymers57,1142
Non-polymers8258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-93 kcal/mol
Surface area21470 Å2
MethodPISA
2
C: 5'/3'-nucleotidase SurE
D: 5'/3'-nucleotidase SurE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7128
Polymers57,1142
Non-polymers5986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-99 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.620, 95.780, 94.750
Angle α, β, γ (deg.)90.00, 100.07, 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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: surE, STM2927 / Plasmid: pRSETC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLysS
References: UniProt: P66881, 5'-nucleotidase, 3'-nucleotidase, exopolyphosphatase

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Non-polymers , 6 types, 1399 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1385 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.2M sodium citrate tribasic dihydrate, 0.1M Tris (pH 8.5), 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2013 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.6→24.89 Å / Num. obs: 184243 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 21.479 Å2 / Rsym value: 0.054 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RYU

4ryu


Resolution: 1.6→24.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.671 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20798 9164 5 %RANDOM
Rwork0.17498 175028 --
obs0.17663 175028 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20.15 Å2
2--0.04 Å20 Å2
3----0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.6→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7656 0 90 1385 9131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.9711267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1851099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1423.908348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.302151194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7551560
X-RAY DIFFRACTIONr_chiral_restr0.1110.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216412
X-RAY DIFFRACTIONr_gen_planes_other
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 663 -
Rwork0.304 12583 -
obs--98.07 %

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