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- PDB-3zie: SepF-like protein from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 3zie
TitleSepF-like protein from Archaeoglobus fulgidus
ComponentsSEPF-LIKE PROTEIN
KeywordsCELL CYCLE
Function / homologyCell 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 / DUF552 domain-containing protein
Function and homology information
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / 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 / struct_ncs_dom_lim
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_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
C: SEPF-LIKE PROTEIN
D: SEPF-LIKE PROTEIN
E: SEPF-LIKE PROTEIN
F: SEPF-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)58,5436
Polymers58,5436
Non-polymers00
Water6,702372
1
A: SEPF-LIKE PROTEIN
B: SEPF-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,5142
Polymers19,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-17.9 kcal/mol
Surface area8790 Å2
MethodPISA
2
E: SEPF-LIKE PROTEIN
F: SEPF-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,5142
Polymers19,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-18.7 kcal/mol
Surface area8640 Å2
MethodPISA
3
C: SEPF-LIKE PROTEIN
D: SEPF-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,5142
Polymers19,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-18.8 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.020, 64.090, 82.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 39 - 116 / Label seq-ID: 3 - 80

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper:
IDCodeMatrixVector
1given(-0.6902, -0.7222, -0.0443), (0.7231, 0.6863, 0.07793), (-0.02588, 0.08582, -0.996)110, 47.56, -10.6
2given(-0.5361, 0.8441, -0.01107), (-0.8401, -0.5347, -0.09167), (-0.0833, -0.03984, 0.9957)51.75, 89.43, 34.62
3given(0.9817, -0.1875, 0.0322), (-0.1878, -0.9822, 0.007406), (0.03024, -0.01332, -0.9995)7.808, 73.2, -39.73
4given(-0.4908, 0.8693, -0.05946), (0.8702, 0.4925, 0.01724), (0.04427, -0.04328, -0.9981)45.58, -90.93, -28.64
5given(-0.2879, -0.9561, 0.05507), (0.9576, -0.287, 0.02468), (-0.007793, 0.05984, 0.9982)144.9, -49.67, 13.23

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Components

#1: Protein
SEPF-LIKE PROTEIN


Mass: 9757.095 Da / Num. of mol.: 6 / Fragment: C-TERMINAL DOMAIN, RESIDUES 37-122 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O29476
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.36 Å3/Da / Density % sol: 47.94 % / Description: NONE
Crystal growDetails: 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE PH 4.5, 30 %W/V PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793, 0.9798
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97981
ReflectionResolution: 1.96→27 Å / Num. obs: 39136 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 22.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 3.482 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24416 1942 5 %RANDOM
Rwork0.188 ---
obs0.19073 37158 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.553 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2--0.61 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 0 0 372 4331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223995
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0551.995391
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1735494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.61824.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81415781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9941536
X-RAY DIFFRACTIONr_chiral_restr0.1370.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212882
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.253.52470
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09444035
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.28651525
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9936.51356
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 614 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.480.5
2Bmedium positional0.530.5
3Cmedium positional0.650.5
4Dmedium positional0.60.5
5Emedium positional0.640.5
6Fmedium positional0.570.5
1Amedium thermal1.522
2Bmedium thermal1.72
3Cmedium thermal2.042
4Dmedium thermal1.692
5Emedium thermal1.852
6Fmedium thermal1.612
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 125 -
Rwork0.187 2730 -
obs--100 %

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