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- PDB-2e6h: Crystal structure of E37A mutant of the stationary phase survival... -

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Basic information

Entry
Database: PDB / ID: 2e6h
TitleCrystal structure of E37A mutant of the stationary phase survival protein SurE from Thermus thermophilus HB8 cocrystallized with manganese and AMP
Components5'-nucleotidase surE
KeywordsHYDROLASE / E37A mutant of 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: 2.1 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 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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. The wild type of this protein is in a dimer-tetramer equilibrium in solution. It is unknown whether the wild type 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)108,09825
Polymers106,2694
Non-polymers1,82921
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19800 Å2
ΔGint-322 kcal/mol
Surface area35210 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)216,19650
Polymers212,5388
Non-polymers3,65842
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area41050 Å2
ΔGint-647 kcal/mol
Surface area68960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.657, 131.657, 130.836
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: 26567.250 Da / Num. of mol.: 4 / Mutation: E37A
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 0.75M ammonium sulfate, 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: Mar 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 76667 / % possible obs: 94.3 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.2
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2 / % possible all: 89.8

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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: 2.1→46.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3162266.35 / 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
Rfree0.25 3673 5.1 %RANDOM
Rwork0.21 ---
obs0.21 72249 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.4745 Å2 / ksol: 0.369542 e/Å3
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.4 Å23.83 Å20 Å2
2--3.4 Å20 Å2
3----6.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7229 0 95 203 7527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it3.161.5
X-RAY DIFFRACTIONc_mcangle_it4.112
X-RAY DIFFRACTIONc_scbond_it4.452
X-RAY DIFFRACTIONc_scangle_it5.742.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 603 5.3 %
Rwork0.247 10773 -
obs--89.9 %
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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