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- PDB-2ek0: Stage V Sporolation Protein S (SPOVS) from Thermus thermophilus Z... -

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Basic information

Entry
Database: PDB / ID: 2ek0
TitleStage V Sporolation Protein S (SPOVS) from Thermus thermophilus Zinc form
ComponentsStage V sporulation protein S (SpoVS) related protein
KeywordsMETAL BINDING PROTEIN / Sporulation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


nucleic acid binding / metal ion binding
Similarity search - Function
Sporulation stage V, protein S / Stage V sporulation protein S (SpoVS) / Alba-like domain / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Stage V sporulation protein S (SpoVS) related protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Stage V Sporolation Protein S (SPOVS) from Thermus thermophilus Zinc form
Authors: Rehse, P.H. / Yokoyama, S.
History
DepositionMar 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 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
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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stage V sporulation protein S (SpoVS) related protein
B: Stage V sporulation protein S (SpoVS) related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5875
Polymers19,3902
Non-polymers1963
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-57 kcal/mol
Surface area9310 Å2
MethodPISA, PQS
2
B: Stage V sporulation protein S (SpoVS) related protein
hetero molecules

B: Stage V sporulation protein S (SpoVS) related protein
hetero molecules

A: Stage V sporulation protein S (SpoVS) related protein
hetero molecules

A: Stage V sporulation protein S (SpoVS) related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,17310
Polymers38,7814
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Buried area3110 Å2
ΔGint-193 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.237, 72.772, 68.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-103-

ZN

21B-104-

HOH

31B-107-

HOH

41B-109-

HOH

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Components

#1: Protein Stage V sporulation protein S (SpoVS) related protein


Mass: 9695.244 Da / Num. of mol.: 2 / Mutation: K22M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q5SK02
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 100mM Na cacodylate, 0.2M Zn Acetate, 35% PEG 200 , pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 13, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→40.5 Å / Num. all: 14849 / Num. obs: 14671 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.066 / Χ2: 1 / Net I/σ(I): 23.5
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.49 / Num. unique all: 1357 / Χ2: 1 / % possible all: 92.6

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Phasing

Phasing MRRfactor: 0.448 / Cor.coef. Fo:Fc: 0.574
Highest resolutionLowest resolution
Rotation3 Å40.46 Å
Translation3 Å40.46 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EH1

2eh1


Resolution: 1.9→40.46 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 682 4.9 %random
Rwork0.229 ---
obs0.229 13512 96.7 %-
all-13973 --
Solvent computationBsol: 94.256 Å2
Displacement parametersBiso mean: 36.964 Å2
Baniso -1Baniso -2Baniso -3
1-2.239 Å20 Å20 Å2
2---0.862 Å20 Å2
3----1.377 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 3 70 1421
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0097181.5
X-RAY DIFFRACTIONc_angle_deg1.639072
X-RAY DIFFRACTIONc_dihedral_angle_d24.534732
X-RAY DIFFRACTIONc_improper_angle_d1.0092.5
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection% reflection
Rfree0.2612 49 -
Rwork0.2406 --
obs-1215 87.67 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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