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- PDB-4xep: Crystal Structure of F222 form of E112A/H234A Mutant of Stationar... -

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Basic information

Entry
Database: PDB / ID: 4xep
TitleCrystal Structure of F222 form of E112A/H234A 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 / 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
PHOSPHATE ION / 5'/3'-nucleotidase SurE
Similarity search - Component
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionDec 24, 2014Deposition 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)28,8587
Polymers28,4901
Non-polymers3686
Water6,359353
1
A: 5'/3'-nucleotidase SurE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,71514
Polymers56,9802
Non-polymers73512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_445-x-1/2,-y-1/2,z1
Buried area9780 Å2
ΔGint-69 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.455, 121.653, 143.401
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-401-

HOH

21A-420-

HOH

31A-486-

HOH

41A-513-

HOH

51A-527-

HOH

61A-529-

HOH

71A-558-

HOH

81A-568-

HOH

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Components

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


Mass: 28490.008 Da / Num. of mol.: 1 / Mutation: E112A, H234A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (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, exopolyphosphatase
#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 / Phosphate


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


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


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.02 M MgCl2 hexahydrate, 22% (w/v) Polyacrylic acid 5100 sodium salt

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 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: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 49090 / % possible obs: 95.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 68.1
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.4 / % possible all: 75.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V4N

2v4n


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.08 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22859 2494 5.1 %RANDOM
Rwork0.18712 46518 --
obs0.18918 46518 95.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.593 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---0.59 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 22 353 2250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022227
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.9643083
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9245319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43424.46894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04715320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7041514
X-RAY DIFFRACTIONr_chiral_restr0.1130.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211766
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: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 139 -
Rwork0.327 2644 -
obs--75.96 %
Refinement TLS params.Method: refined / Origin x: -16.608 Å / Origin y: -20.1 Å / Origin z: 15.605 Å
111213212223313233
T0.1046 Å2-0.024 Å20.0416 Å2-0.0076 Å2-0.0092 Å2--0.0694 Å2
L0.5693 °20.2047 °2-0.2457 °2-1.1433 °2-0.3734 °2--0.6396 °2
S0.1136 Å °-0.0524 Å °0.1137 Å °0.1792 Å °-0.0377 Å °0.0621 Å °-0.2074 Å °0.0542 Å °-0.076 Å °

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