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- PDB-5ckl: Fic protein from Neisseria meningitidis (NmFic) mutant E156R in d... -

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Basic information

Entry
Database: PDB / ID: 5ckl
TitleFic protein from Neisseria meningitidis (NmFic) mutant E156R in dimeric form
ComponentsAdenosine monophosphate-protein transferase NmFic
KeywordsTRANSFERASE / Fic protein / AMP-transferase / dimer
Function / homology
Function and homology information


AMPylase activity / protein adenylylation / protein adenylyltransferase / regulation of cell division / protein homodimerization activity / ATP 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
Protein adenylyltransferase NmFic
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsStanger, F.V. / Schirmer, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification.
Authors: Stanger, F.V. / Burmann, B.M. / Harms, A. / Aragao, H. / Mazur, A. / Sharpe, T. / Dehio, C. / Hiller, S. / Schirmer, T.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine monophosphate-protein transferase NmFic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3505
Polymers22,1511
Non-polymers1984
Water6,395355
1
A: Adenosine monophosphate-protein transferase NmFic
hetero molecules

A: Adenosine monophosphate-protein transferase NmFic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,69910
Polymers44,3022
Non-polymers3978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_585x,-y+3,-z1
Buried area2740 Å2
ΔGint-53 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.333, 50.538, 130.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-203-

CL

21A-541-

HOH

31A-581-

HOH

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Components

#1: Protein Adenosine monophosphate-protein transferase NmFic / AMPylator NmFic


Mass: 22151.230 Da / Num. of mol.: 1 / Mutation: E156R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (strain MC58) (bacteria)
Gene: NMB0255 / Plasmid: pRSFDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7DDR9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.73 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 277.15 K / Method: batch mode / pH: 7.8 / Details: 10 mM Tris pH 7.8, 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.99→65.07 Å / Num. obs: 129938 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.013 / Net I/σ(I): 28.3 / Num. measured all: 839712
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
0.99-1.016.30.6113.33944662180.830.25897.4
5.42-65.076.10.013103.9565392910.00699.1

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s6a

3s6a


Resolution: 0.99→65.07 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.382 / SU ML: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.016 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1246 6534 5 %RANDOM
Rwork0.1121 ---
obs0.1127 123331 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.56 Å2 / Biso mean: 12.635 Å2 / Biso min: 4.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.28 Å2
Refinement stepCycle: final / Resolution: 0.99→65.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 9 362 1869
Biso mean--24.15 28.67 -
Num. residues----181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0191717
X-RAY DIFFRACTIONr_bond_other_d0.0030.021626
X-RAY DIFFRACTIONr_angle_refined_deg2.21.9462332
X-RAY DIFFRACTIONr_angle_other_deg1.11133736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2255217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80623.81497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91815321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7451517
X-RAY DIFFRACTIONr_chiral_restr0.1560.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022064
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02447
X-RAY DIFFRACTIONr_mcbond_it1.8990.856817
X-RAY DIFFRACTIONr_mcbond_other1.5580.851816
X-RAY DIFFRACTIONr_mcangle_it2.0991.2861051
X-RAY DIFFRACTIONr_rigid_bond_restr7.73833342
X-RAY DIFFRACTIONr_sphericity_free36.905513
X-RAY DIFFRACTIONr_sphericity_bonded13.63853648
LS refinement shellResolution: 0.99→1.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 500 -
Rwork0.195 8771 -
all-9271 -
obs--97.24 %

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