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- PDB-2e6g: Crystal structure of the stationary phase survival protein SurE f... -

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Basic information

Entry
Database: PDB / ID: 2e6g
TitleCrystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8 in complex with phosphate
Components5'-nucleotidase surE
KeywordsHYDROLASE / SurE protein / complexed with phosphate ion
Function / homology
Function and homology information


3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase 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
PHOSPHATE ION / 5'-nucleotidase SurE
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 12 chain(s) ...BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 12 chain(s) forming three tetramers. 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
E: 5'-nucleotidase surE
F: 5'-nucleotidase surE
G: 5'-nucleotidase surE
H: 5'-nucleotidase surE
I: 5'-nucleotidase surE
J: 5'-nucleotidase surE
K: 5'-nucleotidase surE
L: 5'-nucleotidase surE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,87837
Polymers319,50312
Non-polymers2,37425
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-nucleotidase surE
F: 5'-nucleotidase surE
G: 5'-nucleotidase surE
H: 5'-nucleotidase surE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,26112
Polymers106,5014
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17790 Å2
ΔGint-156 kcal/mol
Surface area34480 Å2
MethodPISA, PQS
3
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)107,26112
Polymers106,5014
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17600 Å2
ΔGint-154 kcal/mol
Surface area33170 Å2
MethodPISA, PQS
4
I: 5'-nucleotidase surE
J: 5'-nucleotidase surE
K: 5'-nucleotidase surE
L: 5'-nucleotidase surE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,35613
Polymers106,5014
Non-polymers8559
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17510 Å2
ΔGint-162 kcal/mol
Surface area33580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.642, 196.077, 253.852
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.: 12
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20% ethylene glycol, 13% PEG3350, 50mM NaH2PO4, 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: Jun 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 94656 / % possible obs: 99.9 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 4.2 / % possible all: 99.7

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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: 2.6→45.53 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1808183.89 / 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
Rfree0.284 4728 5 %RANDOM
Rwork0.218 ---
obs0.218 94263 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.4938 Å2 / ksol: 0.317988 e/Å3
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2---7.95 Å20 Å2
3---9.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.6→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21146 0 125 86 21357
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it3.611.5
X-RAY DIFFRACTIONc_mcangle_it5.42
X-RAY DIFFRACTIONc_scbond_it5.12
X-RAY DIFFRACTIONc_scangle_it6.692.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 789 5.1 %
Rwork0.293 14755 -
obs--99.8 %
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.param

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