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- PDB-1j9k: CRYSTAL STRUCTURE OF SURE PROTEIN FROM T.MARITIMA IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 1j9k
TitleCRYSTAL STRUCTURE OF SURE PROTEIN FROM T.MARITIMA IN COMPLEX WITH TUNGSTATE
ComponentsSTATIONARY PHASE SURVIVAL PROTEIN
KeywordsUNKNOWN FUNCTION / Tungstate complex / 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
TUNGSTATE(VI)ION / 5'-nucleotidase SurE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSuh, S.W. / Lee, J.Y. / Kwak, J.E. / Moon, J.
Citation
Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure and functional analysis of the SurE protein identify a novel phosphatase family.
Authors: Lee, J.Y. / Kwak, J.E. / Moon, J. / Eom, S.H. / Liong, E.C. / Pedelacq, J.D. / Berendzen, J. / Suh, S.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray crystallographic analysis of the surE protein from Thermotoga maritima
Authors: Kwak, J.E. / Ha, K.S. / Lee, J.Y. / Im, Y.J. / Park, S.H. / Eom, S.H. / Suh, S.W.
History
DepositionMay 27, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 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 / pdbx_struct_conn_angle / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STATIONARY PHASE SURVIVAL PROTEIN
B: STATIONARY PHASE SURVIVAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2678
Polymers56,2142
Non-polymers1,0526
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: STATIONARY PHASE SURVIVAL PROTEIN
hetero molecules

A: STATIONARY PHASE SURVIVAL PROTEIN
hetero molecules

B: STATIONARY PHASE SURVIVAL PROTEIN
hetero molecules

B: STATIONARY PHASE SURVIVAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,53316
Polymers112,4284
Non-polymers2,10512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Buried area20300 Å2
ΔGint-157 kcal/mol
Surface area36280 Å2
MethodPISA
3
A: STATIONARY PHASE SURVIVAL PROTEIN
hetero molecules

A: STATIONARY PHASE SURVIVAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2678
Polymers56,2142
Non-polymers1,0526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
4
B: STATIONARY PHASE SURVIVAL PROTEIN
hetero molecules

B: STATIONARY PHASE SURVIVAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2678
Polymers56,2142
Non-polymers1,0526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)114.910, 114.910, 78.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein STATIONARY PHASE SURVIVAL PROTEIN


Mass: 28107.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P96112
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 296 K
Details: Kwak, J.E., (2001) Acta Crystallogr., Sect.D, 57, 612.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
2100 mMHEPES1reservoir
3200 mM1reservoirMgCl2
430 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Biso Wilson estimate: 19.6 Å2
Reflection
*PLUS
Lowest resolution: 20 Å

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: surE native form (1J9J)

1j9j


Resolution: 2.1→19.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2102121.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3420 10 %RANDOM
Rwork0.192 ---
obs0.192 34179 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.6173 Å2 / ksol: 0.36425 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.5 Å20 Å2
2--0.09 Å20 Å2
3----0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 42 291 4277
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.721.5
X-RAY DIFFRACTIONc_mcangle_it2.822
X-RAY DIFFRACTIONc_scbond_it2.572
X-RAY DIFFRACTIONc_scangle_it4.022.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.278 539 9.6 %
Rwork0.23 5077 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4EPE.PARAMEPE.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
X-RAY DIFFRACTIONc_mcbond_it1.721.5
X-RAY DIFFRACTIONc_scbond_it2.572
X-RAY DIFFRACTIONc_mcangle_it2.822
X-RAY DIFFRACTIONc_scangle_it4.022.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.23

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