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- PDB-3zlm: Fic protein from Neisseria meningitidis mutant E186G in complex w... -

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Basic information

Entry
Database: PDB / ID: 3zlm
TitleFic protein from Neisseria meningitidis mutant E186G in complex with AMPPNP
ComponentsADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE NMFIC
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: 2 Å
AuthorsGoepfert, A. / Schirmer, T.
CitationJournal: Plos One / Year: 2013
Title: Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold.
Authors: Goepfert, A. / Stanger, F.V. / Dehio, C. / Schirmer, T.
History
DepositionFeb 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE NMFIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5823
Polymers22,0511
Non-polymers5312
Water2,468137
1
A: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE NMFIC
hetero molecules

A: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE NMFIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1636
Polymers44,1022
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area3560 Å2
ΔGint-36 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.080, 149.080, 76.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-27-

GLU

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Components

#1: Protein ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE NMFIC / AMPYLATOR NMFIC / FIC PROTEIN


Mass: 22051.088 Da / Num. of mol.: 1 / Fragment: RESIDUES 11-191 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI
References: UniProt: Q7DDR9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 78.8 % / Description: NONE
Crystal growpH: 9
Details: 4M POTASSIUM FORMATE, 0.1M BIS-TRIS PROPANE PH 9.0, 2% W/V PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS-2M-F / Detector: PIXEL / Date: May 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.32 Å / Num. obs: 34254 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 21.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.91
Reflection shellResolution: 2→2.1 Å / Redundancy: 22.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G03

2g03


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.915 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19588 1720 5 %RANDOM
Rwork0.1781 ---
obs0.179 32487 99.88 %-
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 mean: 45.197 Å2
Baniso -1Baniso -2Baniso -3
1--3.95 Å2-1.98 Å20 Å2
2---3.95 Å20 Å2
3---5.93 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 32 137 1621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221523
X-RAY DIFFRACTIONr_bond_other_d0.0010.021047
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9822061
X-RAY DIFFRACTIONr_angle_other_deg0.8432533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8715180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28924.26882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06915274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1571512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02327
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.511.5880
X-RAY DIFFRACTIONr_mcbond_other0.1011.5365
X-RAY DIFFRACTIONr_mcangle_it1.01921415
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7333643
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9054.5644
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 125 -
Rwork0.282 2337 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: -44.8223 Å / Origin y: -47.9121 Å / Origin z: -12.1776 Å
111213212223313233
T0.105 Å20.0692 Å20.0147 Å2-0.0703 Å2-0.0364 Å2--0.09 Å2
L1.8362 °2-0.9111 °2-0.0024 °2-3.4205 °20.0961 °2--0.8757 °2
S-0.0529 Å °-0.093 Å °0.094 Å °0.1912 Å °0.0992 Å °0.0322 Å °-0.0963 Å °-0.037 Å °-0.0463 Å °

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