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- PDB-7cb8: Structure of a FIC-domain protein from Mycobacterium marinum in c... -

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Basic information

Entry
Database: PDB / ID: 7cb8
TitleStructure of a FIC-domain protein from Mycobacterium marinum in complex with CDP
ComponentsFic-domain containing protein
KeywordsTOXIN / Fic protein / Cytidylyltransferase / nucleotidyltransferase activity
Function / homology
Function and homology information


AMPylase activity / ATP binding / membrane
Similarity search - Function
Fido domain-containing protein / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile.
Similarity search - Domain/homology
ACETATE ION / CYTIDINE-5'-DIPHOSPHATE / Fido domain-containing protein
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKumar, S. / Singh, A. / Penmatsa, A. / Surolia, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5012/MED/29/419/2012 India
Department of Biotechnology (DBT, India)BT/PR24443/MED/2a/1220/2017 India
CitationJournal: To Be Published
Title: Structure of of a FIC-domain protein from Mycobacterium marinum
Authors: Kumar, S. / Singh, A. / Penmatsa, A. / Surolia, A.
History
DepositionJun 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fic-domain containing protein
B: Fic-domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,72521
Polymers90,7772
Non-polymers1,94819
Water4,324240
1
A: Fic-domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,31310
Polymers45,3881
Non-polymers9259
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fic-domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,41211
Polymers45,3881
Non-polymers1,02410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.066, 107.900, 110.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fic-domain containing protein


Mass: 45388.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: MMAR_0586 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HP08

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Non-polymers , 5 types, 259 molecules

#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.6
Details: 0.2M Ammonium sulfate, 0.1M Sodium acetate trihydrate, and 25% (w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9799 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.6→49.21 Å / Num. obs: 27934 / % possible obs: 97.8 % / Redundancy: 4.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.108 / Rrim(I) all: 0.23 / Net I/σ(I): 6.5
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3389 / CC1/2: 0.605 / Rpim(I) all: 0.46 / Rrim(I) all: 0.992 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575-000)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZCN

3zcn


Resolution: 2.6→48.488 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 1334 4.78 %
Rwork0.1947 --
obs0.1973 27884 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5919 0 121 240 6280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086131
X-RAY DIFFRACTIONf_angle_d1.098348
X-RAY DIFFRACTIONf_dihedral_angle_d12.3723694
X-RAY DIFFRACTIONf_chiral_restr0.056984
X-RAY DIFFRACTIONf_plane_restr0.0081083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.28141360.23162654X-RAY DIFFRACTION99
2.6929-2.80070.34071410.24022635X-RAY DIFFRACTION99
2.8007-2.92820.32261410.24552639X-RAY DIFFRACTION98
2.9282-3.08250.32991230.22922635X-RAY DIFFRACTION98
3.0825-3.27560.28171280.21772619X-RAY DIFFRACTION97
3.2756-3.52850.29011070.2042688X-RAY DIFFRACTION98
3.5285-3.88340.21531350.17932648X-RAY DIFFRACTION97
3.8834-4.4450.23071370.16192643X-RAY DIFFRACTION97
4.445-5.5990.1821410.16672658X-RAY DIFFRACTION96
5.599-48.480.20861450.17722731X-RAY DIFFRACTION94

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