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- PDB-3se5: Fic protein from NEISSERIA MENINGITIDIS mutant delta8 in complex ... -

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Basic information

Entry
Database: PDB / ID: 3se5
TitleFic protein from NEISSERIA MENINGITIDIS mutant delta8 in complex with AMPPNP
ComponentsCell filamentation protein Fic-related protein
KeywordsTRANSFERASE / AMPylation / adenylylation
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein adenylyltransferase NmFic
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGoepfert, A. / Stanger, F. / 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
DepositionJun 10, 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_atoms / 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_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
B: Cell filamentation protein Fic-related protein
C: Cell filamentation protein Fic-related protein
D: Cell filamentation protein Fic-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,13916
Polymers76,8884
Non-polymers3,25112
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-72 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.945, 65.031, 75.995
Angle α, β, γ (deg.)90.000, 107.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cell filamentation protein Fic-related protein


Mass: 19222.021 Da / Num. of mol.: 4
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 AI / References: UniProt: Q7DDR9
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 44% w/v PEG 600, 0.1M Na-citrate, pH 5.6, vapor diffusion, hanging drop, temperature 293K

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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: 295536
ReflectionResolution: 1.7→37.03 Å / Num. obs: 73865 / % possible obs: 97.69 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.8144
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.7-1.793.460.371.97362101047095.43
1.79-1.94.010.282.69402091003396.43
1.9-2.034.020.183.9938059946497.38
2.03-2.194.060.135.536248892897.95
2.19-2.44.130.16.4434352831898.45
2.4-2.694.160.097.3931205749698.57
2.69-3.14.160.0610.1727643664498.98
3.1-3.84.150.0512.0823525566399.12
3.8-5.384.140.0317.5318250440699.38
5.38-37.034.030.0320.869835244398.25

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Processing

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

2g03


Resolution: 1.7→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.713 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3696 5 %RANDOM
Rwork0.159 ---
obs0.16 73329 97.29 %-
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: 75.46 Å2 / Biso mean: 19.233 Å2 / Biso min: 6.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0 Å2-0.4 Å2
2---0.26 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5068 0 204 424 5696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225351
X-RAY DIFFRACTIONr_bond_other_d0.0010.023721
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9977212
X-RAY DIFFRACTIONr_angle_other_deg0.87739014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.975618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24424.103273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65815969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7471544
X-RAY DIFFRACTIONr_chiral_restr0.0770.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021118
X-RAY DIFFRACTIONr_mcbond_it1.9651.53075
X-RAY DIFFRACTIONr_mcbond_other0.7171.51265
X-RAY DIFFRACTIONr_mcangle_it3.13324938
X-RAY DIFFRACTIONr_scbond_it4.64432276
X-RAY DIFFRACTIONr_scangle_it7.3914.52273
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 239 -
Rwork0.236 4556 -
all-4795 -
obs--94.65 %

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