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- PDB-3zec: Fic protein from SHEWANELLA ONEIDENSIS (E73G mutant) in complex w... -

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Basic information

Entry
Database: PDB / ID: 3zec
TitleFic protein from SHEWANELLA ONEIDENSIS (E73G mutant) in complex with AMPPNP
ComponentsADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC
KeywordsTRANSFERASE / AMPYLATION / ADENYLYLATION
Function / homology
Function and homology information


AMPylase activity / protein adenylyltransferase / protein adenylylation / magnesium ion binding / protein homodimerization activity / ATP binding
Similarity search - Function
Fic/DOC N-terminal / Protein adenylyltransferase SoFic-like / : / Fic/DOC family N-terminal / Protein adenylyltransferase SoFic-like, C-terminal domain / Fido domain-containing protein / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile.
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein adenylyltransferase SoFic
Similarity search - Component
Biological speciesSHEWANELLA ONEIDENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionDec 4, 2012Deposition 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_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC
B: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1755
Polymers86,1392
Non-polymers1,0373
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-22.8 kcal/mol
Surface area32780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.320, 80.630, 141.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE SOFIC / AMPYLATOR SOFIC / FIC DOMAIN CONTAINING TRANSCRIPTION REGULATOR


Mass: 43069.316 Da / Num. of mol.: 2 / Fragment: FIC DOMAIN RESIDUES 2-372 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHEWANELLA ONEIDENSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): AI
References: UniProt: Q8E9K5, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.43 Å3/Da / Density % sol: 49.4 % / Description: NONE
Crystal growpH: 7.1 / Details: 22% W/V PEG3350, 0.2M NAF PH 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.66 Å / Num. obs: 42250 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.57
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.33 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EQX

3eqx


Resolution: 2.2→14.993 Å / SU ML: 0.22 / σ(F): 2 / Phase error: 19.68 / Stereochemistry target values: ML
Details: LOCAL TORSION-ANGLE NCS RESTRAINTS AS IMPLEMENTED IN PHENIX HAVE BEEN APPLIED FOR REFINEMENT
RfactorNum. reflection% reflection
Rfree0.2105 1992 4.7 %
Rwork0.1623 --
obs0.1645 42085 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→14.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5922 0 63 695 6680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116193
X-RAY DIFFRACTIONf_angle_d1.1928470
X-RAY DIFFRACTIONf_dihedral_angle_d16.9962381
X-RAY DIFFRACTIONf_chiral_restr0.07983
X-RAY DIFFRACTIONf_plane_restr0.0071074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27850.2961970.20043956X-RAY DIFFRACTION100
2.2785-2.36940.26311960.1943962X-RAY DIFFRACTION100
2.3694-2.47680.21681960.17423944X-RAY DIFFRACTION100
2.4768-2.60670.23831980.16673972X-RAY DIFFRACTION100
2.6067-2.76910.22141970.16793963X-RAY DIFFRACTION100
2.7691-2.98130.21871990.16894008X-RAY DIFFRACTION100
2.9813-3.27850.23541980.17433984X-RAY DIFFRACTION100
3.2785-3.74640.20712000.15564032X-RAY DIFFRACTION100
3.7464-4.69590.16922020.13724067X-RAY DIFFRACTION100
4.6959-14.99340.17832090.15294205X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0468-0.0004-0.26752.2312-0.71490.7179-0.0008-0.39680.01350.6015-0.03210.0209-0.15690.0370.00540.16920.00480.00910.17220.02920.068514.2105-22.44321.7806
20.6739-0.0777-0.00731.76120.36421.7179-0.03720.1033-0.0637-0.2373-0.0542-0.015-0.0409-0.09030.07340.046-0.00530.02790.0687-0.00760.081319.929-20.3618-7.3763
32.0848-0.8723-1.08422.85870.89612.0624-0.03470.165-0.239-0.2312-0.0423-0.03130.1546-0.23920.06420.1077-0.0362-0.01370.08360.00180.127113.0079-36.7761-6.958
40.1773-0.0530.15990.16160.3651.32530.0995-0.1649-0.59480.11550.0231-0.01740.4063-0.2354-0.11650.1462-0.01470.01680.11720.07810.329415.7473-40.643616.0666
50.82350.2861-0.21560.9595-0.04771.1650.0085-0.0288-0.04-0.01630.00910.0255-0.0373-0.0394-0.00740.02010.0202-0.00990.0376-0.00340.040118.5347-23.85021.6547
60.90150.40880.31180.98120.72841.4663-0.37170.3701-0.4916-0.3211-0.38010.14730.0536-0.52520.01070.2634-0.0380.04050.4488-0.40840.208821.1177-33.0688-30.0171
70.2551-0.4428-0.21881.73670.56380.2265-0.0964-0.05530.04510.3187-0.0016-0.0207-0.0451-0.0416-0.00390.2296-0.0079-0.11230.20820.01220.161927.770820.394212.4648
80.45380.10850.30180.85190.30941.5563-0.05950.0730.0902-0.12670.0117-0.0032-0.1142-0.04960.03320.09140.01020.02650.08730.02880.113617.72889.6141-15.7115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 28 THROUGH 72 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 73 THROUGH 131 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 132 THROUGH 160 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 161 THROUGH 292 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 293 THROUGH 370 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 0 THROUGH 27 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 28 THROUGH 370 )

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