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- PDB-8idv: Crystal structure of Fic protein from Mycoplasma mycoides -

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Basic information

Entry
Database: PDB / ID: 8idv
TitleCrystal structure of Fic protein from Mycoplasma mycoides
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 / DI(HYDROXYETHYL)ETHER / protein adenylyltransferase
Function and homology information
Biological speciesMycoplasma mycoides subsp. capri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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
Authors: Zhang, H. / Zhao, H.F.
History
DepositionFeb 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,1179
Polymers90,4974
Non-polymers6205
Water00
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)120.600, 120.600, 165.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.84 Å3/Da / Density % sol: 67.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, 22% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.499→50 Å / Num. obs: 18055 / % possible obs: 95.6 % / Redundancy: 18.5 % / Biso Wilson estimate: 122.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.153 / Rrim(I) all: 0.168 / Net I/σ(I): 10.56
Reflection shellResolution: 3.5→3.71 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.921 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 2873 / CC1/2: 0.793 / Rrim(I) all: 0.966 / % possible all: 88.7

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Processing

Software
NameVersionClassification
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
PHENIX1.10.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→44.19 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.897 / SU B: 35.953 / SU ML: 0.526 / Cross valid method: THROUGHOUT / ESU R Free: 0.658 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29713 1787 9.9 %RANDOM
Rwork0.21373 ---
obs0.22197 16231 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 139.589 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å21.2 Å20 Å2
2--2.41 Å2-0 Å2
3----7.82 Å2
Refinement stepCycle: 1 / Resolution: 3.5→44.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6017 0 40 0 6057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176063
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6268242
X-RAY DIFFRACTIONr_angle_other_deg1.1441.58813921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5525707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.38724.399341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.625151223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2561524
X-RAY DIFFRACTIONr_chiral_restr0.060.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026785
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021451
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_it12.1114.3282855
X-RAY DIFFRACTIONr_mcbond_other12.10614.3272854
X-RAY DIFFRACTIONr_mcangle_it17.95521.4963553
X-RAY DIFFRACTIONr_mcangle_other17.95621.4983554
X-RAY DIFFRACTIONr_scbond_it12.06715.1923286
X-RAY DIFFRACTIONr_scbond_other12.06615.1933287
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.3622.4624690
X-RAY DIFFRACTIONr_long_range_B_refined22.47185
X-RAY DIFFRACTIONr_long_range_B_other22.3997186
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.59 Å
RfactorNum. reflection% reflection
Rfree0.348 133 -
Rwork0.303 1194 -
obs--99.85 %

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