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- PDB-2e6e: Crystal structure of the stationary phase survival protein SurE f... -

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Basic information

Entry
Database: PDB / ID: 2e6e
TitleCrystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8
Components5'-nucleotidase surE
KeywordsHYDROLASE / SurE protein
Function / homology
Function and homology information


3'-nucleotidase activity / exopolyphosphatase activity / : / 5'-nucleotidase / 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: 2.5 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,5014
Polymers106,5014
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13490 Å2
ΔGint-90 kcal/mol
Surface area34270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.222, 68.635, 220.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: 30% ethylene glycol, 1% PEG4000, 0.1M Na acetate, pH 4.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 31508 / % possible obs: 96 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 26.9
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 13.1 / % possible all: 80.9

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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 2E6C

2e6c


Resolution: 2.5→45.63 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2100700.89 / 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
Rfree0.288 1494 5 %RANDOM
Rwork0.222 ---
obs0.222 30178 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.9254 Å2 / ksol: 0.355924 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1-9.51 Å20 Å20 Å2
2---5.35 Å20 Å2
3----4.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 0 78 6737
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.231.5
X-RAY DIFFRACTIONc_mcangle_it3.562
X-RAY DIFFRACTIONc_scbond_it3.172
X-RAY DIFFRACTIONc_scangle_it4.452.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 227 5.3 %
Rwork0.247 4096 -
obs--83.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cis_peptide.paramwater.top
X-RAY DIFFRACTION3WATER_REP.PARAM

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