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- PDB-2e69: Crystal structure of the stationary phase survival protein SurE f... -

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Basic information

Entry
Database: PDB / ID: 2.0E+69
TitleCrystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8 in complex with sulfate
Components5'-nucleotidase surE
KeywordsHYDROLASE / SurE protein
Function / homology
Function and homology information


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
5'-nucleotidase SurE
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIwasaki, W. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the Stationary Phase Survival Protein SurE with Metal Ion and AMP
Authors: Iwasaki, W. / Miki, K.
History
DepositionDec 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) ...BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) forming a tetramer. This protein is in a dimer-tetramer equilibrium in solution. It is unknown whether this protein is functional as a dimer or a tetramer.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-nucleotidase surE
B: 5'-nucleotidase surE
C: 5'-nucleotidase surE
D: 5'-nucleotidase surE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,03020
Polymers106,5014
Non-polymers1,52916
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19040 Å2
ΔGint-337 kcal/mol
Surface area35820 Å2
MethodPISA, PQS
2
A: 5'-nucleotidase surE
B: 5'-nucleotidase surE
C: 5'-nucleotidase surE
D: 5'-nucleotidase surE
hetero molecules

A: 5'-nucleotidase surE
B: 5'-nucleotidase surE
C: 5'-nucleotidase surE
D: 5'-nucleotidase surE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,06040
Polymers213,0028
Non-polymers3,05832
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area40880 Å2
ΔGint-684 kcal/mol
Surface area68840 Å2
MethodPISA
3
A: 5'-nucleotidase surE
B: 5'-nucleotidase surE
C: 5'-nucleotidase surE
D: 5'-nucleotidase surE
hetero molecules

A: 5'-nucleotidase surE
B: 5'-nucleotidase surE
C: 5'-nucleotidase surE
D: 5'-nucleotidase surE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,06040
Polymers213,0028
Non-polymers3,05832
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area39610 Å2
ΔGint-680 kcal/mol
Surface area70120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.825, 131.825, 131.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsprobably tetramer

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Components

#1: Protein
5'-nucleotidase surE / Stationary Phase Survival Protein SurE / Nucleoside 5'-monophosphate phosphohydrolase


Mass: 26625.287 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W92, 5'-nucleotidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris-HCl pH8.5, 0.75M ammonium sulhate, 10% glycerol, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 67207 / % possible obs: 99.9 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ILV

1ilv


Resolution: 2.2→43.06 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3080294.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3412 5.1 %RANDOM
Rwork0.195 ---
obs0.195 67111 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9784 Å2 / ksol: 0.37035 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å23.92 Å20 Å2
2--3.7 Å20 Å2
3----7.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7251 0 82 217 7550
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it3.061.5
X-RAY DIFFRACTIONc_mcangle_it4.092
X-RAY DIFFRACTIONc_scbond_it4.762
X-RAY DIFFRACTIONc_scangle_it5.992.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 568 5.1 %
Rwork0.211 10465 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.paramion.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4water_rep.paramgol.top
X-RAY DIFFRACTION5gol.param

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