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- PDB-3zig: SepF-like protein from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 3zig
TitleSepF-like protein from Pyrococcus furiosus
ComponentsSEPF-LIKE PROTEIN
KeywordsCELL CYCLE
Function / homology
Function and homology information


cell septum assembly
Similarity search - Function
Cell division protein SepF, archaea / SepF-like protein / Cell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein SepF
Similarity search - Component
Biological speciesPYROCOCCUS FURIOSUS COM1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsDuman, R. / Ishikawa, S. / Celik, I. / Ogasawara, N. / Lowe, J. / Hamoen, L.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and Genetic Analyses Reveal the Protein Sepf as a New Membrane Anchor for the Z Ring.
Authors: Duman, R. / Ishikawa, S. / Celik, I. / Strahl, H. / Ogasawara, N. / Troc, P. / Lowe, J. / Hamoen, L.W.
History
DepositionJan 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEPF-LIKE PROTEIN
B: SEPF-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,9922
Polymers18,9922
Non-polymers00
Water52229
1
A: SEPF-LIKE PROTEIN

A: SEPF-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,9922
Polymers18,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_574x,x-y+2,-z-1/61
Buried area1680 Å2
ΔGint-12 kcal/mol
Surface area8850 Å2
MethodPISA
2
B: SEPF-LIKE PROTEIN

B: SEPF-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)18,9922
Polymers18,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_574x,x-y+2,-z-1/61
Buried area1710 Å2
ΔGint-10 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.327, 59.327, 177.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-113-

CYS

21A-2014-

HOH

31B-2009-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 51:112 )
211CHAIN B AND (RESSEQ 51:112 )
112CHAIN A AND (RESSEQ 114:128 )
212CHAIN B AND (RESSEQ 114:128 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.877306, 0.198287, -0.437054), (0.166965, 0.727675, 0.665291), (0.449952, -0.656637, 0.605286)9.3564, 46.3102, 42.7424
2given(0.892401, 0.183658, -0.412176), (0.167554, 0.713255, 0.680583), (0.418981, -0.676415, 0.605738)11.223, 47.1033, 41.8967

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Components

#1: Protein SEPF-LIKE PROTEIN


Mass: 9496.246 Da / Num. of mol.: 2 / Fragment: RESIDUES 46-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS FURIOSUS COM1 (archaea) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: I6V3Q6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.21 Å3/Da / Density % sol: 44.38 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.5, 25% W/V PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→29.58 Å / Num. obs: 7036 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 26.2 % / Biso Wilson estimate: 39.32 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 31.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 14.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.5→29.581 Å / SU ML: 0.4 / σ(F): 1.59 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2888 615 5.1 %
Rwork0.2186 --
obs0.2223 7036 99.98 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.815 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.674 Å20 Å20 Å2
2---5.674 Å20 Å2
3---11.348 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 0 29 1301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081289
X-RAY DIFFRACTIONf_angle_d0.9731737
X-RAY DIFFRACTIONf_dihedral_angle_d13.654509
X-RAY DIFFRACTIONf_chiral_restr0.054225
X-RAY DIFFRACTIONf_plane_restr0.004207
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A481X-RAY DIFFRACTIONPOSITIONAL
12B481X-RAY DIFFRACTIONPOSITIONAL0.056
21A112X-RAY DIFFRACTIONPOSITIONAL
22B112X-RAY DIFFRACTIONPOSITIONAL0.065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.75140.33211770.26712855X-RAY DIFFRACTION100
2.7514-3.14920.38461480.23012869X-RAY DIFFRACTION100
3.1492-3.96610.32011480.22832887X-RAY DIFFRACTION100
3.9661-29.58270.21041420.19452876X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8642-1.4201-0.22561.4612-0.43370.98840.13870.0208-0.4546-0.11850.02290.0356-0.10690.0336-0.15390.12370.0267-0.01520.1749-0.05230.196-20.374843.8822-16.2302
20.7803-0.3179-0.22241.5042-0.37060.9726-0.07520.1272-0.0551-0.1346-0.0205-0.03930.0993-0.04170.05170.11280.01710.04190.134-0.05440.0831-53.059531.0663-24.329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 51:128
2X-RAY DIFFRACTION2CHAIN B AND RESSEQ 51:128

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