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- PDB-2f6s: Structure of cell filamentation protein (fic) from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 2f6s
TitleStructure of cell filamentation protein (fic) from Helicobacter pylori
Componentscell filamentation protein, putative
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / cell filamentation protein / Helicobacter pylori / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein adenylyltransferase / regulation of cell division / transferase activity / metal ion binding
Similarity search - Function
Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / : / protein adenylyltransferase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsCuff, M.E. / Xu, X. / Zheng, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of cell filamentation protein (fic) from Helicobacter pylori
Authors: Cuff, M.E. / Xu, X. / Zheng, H. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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

Downloads & links

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Assembly

Deposited unit
A: cell filamentation protein, putative
B: cell filamentation protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2506
Polymers46,9292
Non-polymers3214
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-100 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.140, 86.140, 164.892
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein cell filamentation protein, putative


Mass: 23464.377 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: fic / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 15645773, UniProt: O25774*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M sodium potassium dihydrogen phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97962, 0.97948
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979621
20.979481
ReflectionResolution: 2.5→50 Å / Num. all: 23887 / Num. obs: 23887 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.565 Å / % possible all: 99.77

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXmodel building
CCP4model building
MLPHAREphasing
DMmodel building
Omodel building
RESOLVEmodel building
Cootmodel building
REFMAC5.2refinement
HKL-3000phasing
SHELXphasing
CCP4phasing
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 11.677 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.243 / ESU R Free: 0.205
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21452 1224 5.1 %RANDOM
Rwork0.16867 ---
all0.17101 23887 --
obs0.17101 22663 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.392 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å21.4 Å20 Å2
2--2.8 Å20 Å2
3----4.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 12 235 3177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223002
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.9774030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4725358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.89324.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.06915580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0521518
X-RAY DIFFRACTIONr_chiral_restr0.10.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022196
X-RAY DIFFRACTIONr_nbd_refined0.2160.21522
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.28
X-RAY DIFFRACTIONr_mcbond_it0.7011.51820
X-RAY DIFFRACTIONr_mcangle_it1.08222872
X-RAY DIFFRACTIONr_scbond_it2.22431303
X-RAY DIFFRACTIONr_scangle_it3.3964.51158
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 95 -
Rwork0.209 1673 -
obs--99.77 %
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)
11.28710.4677-0.55221.8082-0.32023.06550.03940.1893-0.0223-0.2123-0.0610.09950.1719-0.16920.0216-0.15690.05310.0233-0.2055-0.0355-0.304-14.27850.2029.321
21.1490.0122-0.02792.9330.08632.40810.0587-0.17290.04450.3089-0.1042-0.06410.10560.13460.0455-0.20360.0006-0.0071-0.1973-0.0103-0.3089-4.68780.59217.383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 17821 - 200
2X-RAY DIFFRACTION2BB-1 - 17821 - 200

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