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- PDB-8idw: Crystal structure of Fic protein from Mycoplasma mycoides in comp... -

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Basic information

Entry
Database: PDB / ID: 8idw
TitleCrystal structure of Fic protein from Mycoplasma mycoides in complex with AMPPNP
ComponentsCell filamentation protein Fic
KeywordsTRANSFERASE / Fic protein / AMP transferase
Function / homologyFido-like domain superfamily / protein adenylyltransferase / Fic/DOC family / Fido domain / Fido domain profile. / transferase activity / AMP PHOSPHORAMIDATE / protein adenylyltransferase
Function and homology information
Biological speciesMycoplasma mycoides subsp. capri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å
AuthorsZhang, H. / Zhao, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970152 China
CitationJournal: To Be Published
Title: Crystal structure of Fic protein from Mycoplasma mycoides in complex with AMPPNP
Authors: Zhang, H. / Zhao, H.F.
History
DepositionFeb 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell filamentation protein Fic
B: Cell filamentation protein Fic
C: Cell filamentation protein Fic
D: Cell filamentation protein Fic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,57515
Polymers90,4974
Non-polymers2,07811
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.506, 68.299, 121.006
Angle α, β, γ (deg.)90.00, 110.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cell filamentation protein Fic


Mass: 22624.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma mycoides subsp. capri (bacteria)
Gene: MMC68J_00751 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Z7PMX0
#2: Chemical
ChemComp-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N6O9P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesium chloride, 0.1 M BIS-TRIS, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 41783 / % possible obs: 99.7 % / Redundancy: 35.9 % / Biso Wilson estimate: 37.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.085 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.45 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6076 / CC1/2: 0.903 / Rrim(I) all: 0.479 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.304→34.765 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 2001 4.8 %
Rwork0.2035 --
obs0.2058 41705 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.304→34.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6134 0 130 279 6543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016401
X-RAY DIFFRACTIONf_angle_d1.138630
X-RAY DIFFRACTIONf_dihedral_angle_d14.4843844
X-RAY DIFFRACTIONf_chiral_restr0.056969
X-RAY DIFFRACTIONf_plane_restr0.0051063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.304-2.36160.32421450.25662813X-RAY DIFFRACTION99
2.3616-2.42540.29171400.24672824X-RAY DIFFRACTION99
2.4254-2.49680.33261330.24022821X-RAY DIFFRACTION100
2.4968-2.57740.28711470.22822803X-RAY DIFFRACTION100
2.5774-2.66940.30311500.23432825X-RAY DIFFRACTION100
2.6694-2.77630.33431330.23092829X-RAY DIFFRACTION100
2.7763-2.90260.311440.23742843X-RAY DIFFRACTION100
2.9026-3.05550.29171440.23292811X-RAY DIFFRACTION100
3.0555-3.24680.29831410.23682866X-RAY DIFFRACTION100
3.2468-3.49730.25861460.2132827X-RAY DIFFRACTION100
3.4973-3.84890.2211400.19982843X-RAY DIFFRACTION100
3.8489-4.40480.25731400.17092867X-RAY DIFFRACTION100
4.4048-5.5460.21511460.17482847X-RAY DIFFRACTION99
5.546-34.760.16351520.16662885X-RAY DIFFRACTION98

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