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- PDB-4x2e: Clostridium difficile wild type Fic protein -

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Basic information

Entry
Database: PDB / ID: 4x2e
TitleClostridium difficile wild type Fic protein
ComponentsFic family protein putative filamentation induced by cAMP protein
KeywordsTRANSFERASE
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
Fido domain-containing protein / 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
Fic family protein putative filamentation induced by cAMP protein
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.104 Å
AuthorsJorgensen, R. / Dedic, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research11-104831/FSS Denmark
CitationJournal: To Be Published
Title: Structure of wild type Clostridium difficile Fic_0569 at 3.1 Angstroms resolution
Authors: Jorgensen, R. / Dedic, E. / Alsarraf, H. / Welner, D. / van Leeuwen, H.C. / Oestergaard, O.
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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: Fic family protein putative filamentation induced by cAMP protein
B: Fic family protein putative filamentation induced by cAMP protein
C: Fic family protein putative filamentation induced by cAMP protein
D: Fic family protein putative filamentation induced by cAMP protein


Theoretical massNumber of molelcules
Total (without water)109,4814
Polymers109,4814
Non-polymers00
Water00
1
A: Fic family protein putative filamentation induced by cAMP protein

B: Fic family protein putative filamentation induced by cAMP protein


Theoretical massNumber of molelcules
Total (without water)54,7402
Polymers54,7402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
2
B: Fic family protein putative filamentation induced by cAMP protein

A: Fic family protein putative filamentation induced by cAMP protein


Theoretical massNumber of molelcules
Total (without water)54,7402
Polymers54,7402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_545x+1/2,-y-1/2,-z1
3
D: Fic family protein putative filamentation induced by cAMP protein

C: Fic family protein putative filamentation induced by cAMP protein


Theoretical massNumber of molelcules
Total (without water)54,7402
Polymers54,7402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
4
C: Fic family protein putative filamentation induced by cAMP protein

D: Fic family protein putative filamentation induced by cAMP protein


Theoretical massNumber of molelcules
Total (without water)54,7402
Polymers54,7402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1270 Å2
ΔGint-8 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.420, 157.370, 262.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERMETMETchain AAA4 - 2304 - 230
2SERSERLEULEUchain BBB4 - 2344 - 234
3SERSERTRPTRPchain CCC4 - 2324 - 232
4ASPASPVALVALchain DDD7 - 2277 - 227

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Components

#1: Protein
Fic family protein putative filamentation induced by cAMP protein


Mass: 27370.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Strain: R20291 / Gene: CDR20291_0569
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C9YJ22

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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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 % (w/v) PEG 8000, 0.2 M MgCl2, 0.1 M Hepes pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 6, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 3.1→45.93 Å / Num. obs: 22213 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.02 % / Biso Wilson estimate: 51.86 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.173 / Χ2: 0.947 / Net I/σ(I): 9.71 / Num. measured all: 178303
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.1-3.28.410.8211.0691.716816200019991.1499.9
3.2-3.30.9060.722.4514320171917190.769100
3.3-3.50.9380.5173.6424604294329430.551100
3.5-40.9680.2996.5541639503450340.319100
4-50.9890.15312.5839715502950280.164100
5-60.9880.1314.5817688226222610.139100
6-80.9950.09317.8613704181118100.199.9
8-100.9960.06124.5148216746740.066100
100.9980.04926.0649967597450.05398.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.1 Å45.93 Å
Translation3.1 Å45.93 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X2C

4x2c


Resolution: 3.104→19.945 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 1026 5.02 %Random Selection
Rwork0.2432 19428 --
obs0.2454 20454 92.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.78 Å2 / Biso mean: 56.8864 Å2 / Biso min: 18.36 Å2
Refinement stepCycle: final / Resolution: 3.104→19.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6561 0 0 0 6561
Num. residues----797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036700
X-RAY DIFFRACTIONf_angle_d0.7339075
X-RAY DIFFRACTIONf_chiral_restr0.031035
X-RAY DIFFRACTIONf_plane_restr0.0031142
X-RAY DIFFRACTIONf_dihedral_angle_d12.1232442
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3753X-RAY DIFFRACTION11.065TORSIONAL
12B3753X-RAY DIFFRACTION11.065TORSIONAL
13C3753X-RAY DIFFRACTION11.065TORSIONAL
14D3753X-RAY DIFFRACTION11.065TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.104-3.2670.3639810.35161467154850
3.267-3.47070.36171540.291829273081100
3.4707-3.73710.34171560.278529553111100
3.7371-4.11020.27541560.257829723128100
4.1102-4.69810.28871570.227829693126100
4.6981-5.89370.28041580.223830073165100
5.8937-19.94570.21881640.198131313295100
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)
11.5583-1.33050.64344.0551-0.71961.71820.07960.02210.3306-0.0265-0.0804-0.1399-0.264-0.0877-0.03710.32680.0463-0.0195-0.0269-0.0410.4824-21.6747-18.1285-18.758
21.08610.30710.21612.73410.27292.5642-0.1127-0.08540.51920.0398-0.22480.3443-0.4504-0.1691-0.10110.3299-0.0399-0.1170.08470.02530.60114.3124-17.879810.2936
31.74341.2154-0.14523.1744-1.01791.10120.0912-0.3854-0.02150.5524-0.3452-0.5782-0.11230.1445-0.17890.5514-0.3608-0.15080.27420.08160.4976-34.1594-20.762135.0592
41.76951.10331.10271.9240.43731.22310.3243-0.58850.08190.8423-0.48570.5146-0.0673-0.3120.03870.8526-0.50680.19810.7752-0.07240.5108-5.8411-51.360144.834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 230 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 4 through 234 )B0
3X-RAY DIFFRACTION3chain 'C' and (resid 4 through 232 )C0
4X-RAY DIFFRACTION4chain 'D' and (resid 7 through 230 )D0

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