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- PDB-4da2: The structure of Pyrococcus Furiosus SfsA in complex with Ca2+ -

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Basic information

Entry
Database: PDB / ID: 4da2
TitleThe structure of Pyrococcus Furiosus SfsA in complex with Ca2+
ComponentsSugar fermentation stimulation protein homolog
KeywordsDNA BINDING PROTEIN / OB fold / PD-(D/E)xK domain / nuclease
Function / homology
Function and homology information


OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #580 / Trna Endonuclease; Chain: A, domain 1 - #60 / Sugar fermentation stimulation protein / Sugar fermentation stimulation protein, C-terminal / SfsA, N-terminal OB domain / Sugar fermentation stimulation protein RE domain / SfsA N-terminal OB domain / Trna Endonuclease; Chain: A, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #580 / Trna Endonuclease; Chain: A, domain 1 - #60 / Sugar fermentation stimulation protein / Sugar fermentation stimulation protein, C-terminal / SfsA, N-terminal OB domain / Sugar fermentation stimulation protein RE domain / SfsA N-terminal OB domain / Trna Endonuclease; Chain: A, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sugar fermentation stimulation protein homolog
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsBaker, P.J. / Allen, F.L.
CitationJournal: To be Published
Title: The structure of SfsA and its DNA complex; A DNA/RNA nuclease with a novel domain combination
Authors: Allen, F.L. / Akerboom, J. / Bliss, S.J. / Blombach, F. / Sedelnikova, S.E. / van der Oost, J. / Baker, P.J.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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.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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Sugar fermentation stimulation protein homolog
B: Sugar fermentation stimulation protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6196
Polymers52,4582
Non-polymers1604
Water2,954164
1
A: Sugar fermentation stimulation protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3093
Polymers26,2291
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sugar fermentation stimulation protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3093
Polymers26,2291
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.017, 46.017, 194.575
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Sugar fermentation stimulation protein homolog


Mass: 26229.098 Da / Num. of mol.: 2 / Mutation: L120I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1198, sfsA / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U1K8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 4.6
Details: 30% (w/v) PEG 3350, 0.2 M calcium acetate, 0.01 M sodium acetate and 0.22 M potassium chloride pH 4.6, vapor diffusion, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.975564
SYNCHROTRONESRF ID2920.9793, 0.9795, 0.9755
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 16, 2008
DECTRIS PILATUS 6M2PIXELMay 11, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond Beamline I03SINGLE WAVELENGTHMx-ray1
2liquid nitrogen cooled channel-cut silicon monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9755641
20.97931
30.97951
40.97551
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.624
11K, H, -L20.376
ReflectionResolution: 1.8→64.8 Å / Num. all: 42809 / Num. obs: 42809 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.45 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
GDAdata collection
RefinementMethod to determine structure: MAD / Resolution: 1.8→196.19 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.422 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1716 2120 5 %RANDOM
Rwork0.1361 ---
all0.14 42809 --
obs0.1379 42741 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 449.72 Å2 / Biso mean: 25.0569 Å2 / Biso min: 5.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0 Å20 Å2
2---0.84 Å2-0 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→196.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3676 0 4 164 3844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223736
X-RAY DIFFRACTIONr_angle_refined_deg1.3742.015004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63622.179156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94815752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0631542
X-RAY DIFFRACTIONr_chiral_restr0.0940.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212724
X-RAY DIFFRACTIONr_mcbond_it8.6122288
X-RAY DIFFRACTIONr_mcangle_it8.95433686
X-RAY DIFFRACTIONr_scbond_it34.05821448
X-RAY DIFFRACTIONr_scangle_it27.4631318
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 135 -
Rwork0.181 3053 -
all-3188 -
obs--98.09 %

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