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- PDB-3s6a: Fic protein from NEISSERIA MENINGITIDIS in complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 3s6a
TitleFic protein from NEISSERIA MENINGITIDIS in complex with AMPPNP
ComponentsCell filamentation protein Fic-related protein
KeywordsTRANSFERASE / AMPylation / adenylylation
Function / homology
Function and homology information


AMPylase activity / protein adenylyltransferase / protein adenylylation / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein adenylyltransferase NmFic
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsStanger, F. / Goepfert, A. / Schirmer, T.
CitationJournal: Nature / Year: 2012
Title: Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins.
Authors: Engel, P. / Goepfert, A. / Stanger, F.V. / Harms, A. / Schmidt, A. / Schirmer, T. / Dehio, C.
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / 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 / _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

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Assembly

Deposited unit
A: Cell filamentation protein Fic-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6292
Polymers22,1231
Non-polymers5061
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cell filamentation protein Fic-related protein
hetero molecules

A: Cell filamentation protein Fic-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2594
Polymers44,2462
Non-polymers1,0122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area3370 Å2
ΔGint-19 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.960, 148.960, 75.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

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Components

#1: Protein Cell filamentation protein Fic-related protein


Mass: 22123.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: serogroup B / Gene: NMB0255 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DDR9
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 5.8 Å3/Da / Density % sol: 78.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5% 2-propanol, 0.1M MES, 0.1M Ca-acetate, pH 6.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber: 371482
ReflectionResolution: 2.15→65.35 Å / Num. all: 27218 / Num. obs: 27218 / % possible obs: 99.11 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.65 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.5111
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.15-2.278.810.471.632385367893.93
2.27-2.414.040.372.03522373721100
2.4-2.5714.630.282.69514643517100
2.57-2.7814.690.194.02481763280100
2.78-3.0414.730.135.86448733046100
3.04-3.414.640.088.84402362748100
3.4-3.9314.570.078.75356992451100
3.93-4.8114.390.086.92303272108100
4.81-6.814.020.0412.79234241671100
6.8-65.3512.690.0221.411266199899.91

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16 2010/01/06data scaling
MOSFLMdata reduction
FFTphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2g03

2g03


Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.463 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1290 5.1 %RANDOM
Rwork0.188 ---
all0.19 25536 --
obs0.19 25536 99.96 %-
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 max: 82.53 Å2 / Biso mean: 38.518 Å2 / Biso min: 14.44 Å2
Baniso -1Baniso -2Baniso -3
1--3.57 Å2-1.78 Å20 Å2
2---3.57 Å20 Å2
3---5.35 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 27 184 1676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221521
X-RAY DIFFRACTIONr_bond_other_d0.0010.021048
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9792053
X-RAY DIFFRACTIONr_angle_other_deg0.83332534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2065177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28424.26882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19515276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3161512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021676
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
X-RAY DIFFRACTIONr_mcbond_it1.1751.5880
X-RAY DIFFRACTIONr_mcbond_other0.2971.5364
X-RAY DIFFRACTIONr_mcangle_it2.25921413
X-RAY DIFFRACTIONr_scbond_it3.7123641
X-RAY DIFFRACTIONr_scangle_it5.9714.5640
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 76 -
Rwork0.31 1726 -
all-1802 -
obs--99.56 %

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