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- PDB-5cgl: Fic protein from Neisseria meningitidis (NmFic) mutant E102R in d... -

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Basic information

Entry
Database: PDB / ID: 5cgl
TitleFic protein from Neisseria meningitidis (NmFic) mutant E102R 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
DI(HYDROXYETHYL)ETHER / Protein adenylyltransferase NmFic
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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 9, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Adenosine monophosphate-protein transferase NmFic
B: Adenosine monophosphate-protein transferase NmFic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5154
Polymers44,3022
Non-polymers2122
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint3 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.557, 81.905, 97.525
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERchain AAA13 - 18910 - 186
2LYSLYSchain BBB12 - 1899 - 186

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Components

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


Mass: 22151.230 Da / Num. of mol.: 2 / Fragment: UNP residues 11-191 / Mutation: E102R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: NMB0255 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7DDR9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.53 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 8% (v/v) Tacsimate pH 6.0, 20% (w/v) PEG 33505

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→97.53 Å / Num. obs: 16845 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 33.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.03 / Net I/σ(I): 19.8 / Num. measured all: 120108
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
2.35-2.437.40.4614.61204216360.9260.182100
9.1-97.536.30.02753.621703450.9990.01299.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.46 Å48.76 Å
Translation4.46 Å48.76 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s6a

3s6a


Resolution: 2.35→48.763 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 848 5.05 %
Rwork0.199 15959 -
obs0.2006 16807 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.27 Å2 / Biso mean: 38.5879 Å2 / Biso min: 18.49 Å2
Refinement stepCycle: final / Resolution: 2.35→48.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 34 146 2871
Biso mean--54.17 39.43 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022789
X-RAY DIFFRACTIONf_angle_d0.5323753
X-RAY DIFFRACTIONf_chiral_restr0.023403
X-RAY DIFFRACTIONf_plane_restr0.002486
X-RAY DIFFRACTIONf_dihedral_angle_d14.6041068
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1594X-RAY DIFFRACTION6.307TORSIONAL
12B1594X-RAY DIFFRACTION6.307TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3501-2.49730.24911320.241426222754
2.4973-2.69010.26551380.226426042742
2.6901-2.96080.26251580.234626112769
2.9608-3.38920.29131320.228426462778
3.3892-4.26960.20111330.179426812814
4.2696-48.7730.19761550.168327952950
Refinement TLS params.Method: refined / Origin x: -10.4828 Å / Origin y: 27.1273 Å / Origin z: -11.5378 Å
111213212223313233
T0.2487 Å2-0.0054 Å20.0186 Å2-0.2487 Å2-0.0187 Å2--0.2523 Å2
L0.8796 °2-1.1346 °20.5844 °2-1.5377 °2-1.1258 °2--0.862 °2
S-0.0383 Å °-0.0212 Å °-0.0178 Å °0.132 Å °0.1004 Å °0.079 Å °-0.1187 Å °-0.0983 Å °-0.0669 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA13 - 189
2X-RAY DIFFRACTION1allB12 - 189
3X-RAY DIFFRACTION1allS2 - 177
4X-RAY DIFFRACTION1allC1 - 2

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