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- PDB-7f2u: FmnB complexed with ADP -

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Basic information

Entry
Database: PDB / ID: 7f2u
TitleFmnB complexed with ADP
ComponentsFAD:protein FMN transferase
KeywordsTRANSFERASE / Inhibitor / ADP / FMN transferase
Function / homology
Function and homology information


FAD:protein FMN transferase / transferase activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Flavin transferase ApbE / ApbE family / ApbE-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FAD:protein FMN transferase
Similarity search - Component
Biological speciesListeria monocytogenes serotype 1/2a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.984 Å
AuthorsCheng, W. / Zheng, Y.H.
CitationJournal: MedComm (2020) / Year: 2022
Title: Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes.
Authors: Zheng, Y. / Yan, W. / Dou, C. / Zhou, D. / Chen, Y. / Jin, Y. / Yang, L. / Zeng, X. / Cheng, W.
History
DepositionJun 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

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Assembly

Deposited unit
A: FAD:protein FMN transferase
B: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3788
Polymers75,4272
Non-polymers9526
Water7,098394
1
A: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1894
Polymers37,7131
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-29 kcal/mol
Surface area14450 Å2
MethodPISA
2
B: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1894
Polymers37,7131
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-28 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.020, 66.489, 109.100
Angle α, β, γ (deg.)90.000, 95.610, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein FAD:protein FMN transferase / Flavin transferase


Mass: 37713.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serotype 1/2a (strain 10403S) (bacteria)
Strain: 10403S / Gene: LMRG_02181
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H3GJF7, FAD:protein FMN transferase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium formate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.984→27.58 Å / Num. obs: 43550 / % possible obs: 91.55 % / Redundancy: 1.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.04182 / Net I/σ(I): 11.68
Reflection shellResolution: 1.984→2.055 Å / Num. unique obs: 3092 / CC1/2: 0.867

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ESA

7esa


Resolution: 1.984→27.58 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2482 --
Rwork0.2038 --
obs-43550 91.55 %
Displacement parametersBiso mean: 28.01 Å2
Refinement stepCycle: LAST / Resolution: 1.984→27.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5066 0 4 394 5464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095157
X-RAY DIFFRACTIONf_angle_d1.17866960
X-RAY DIFFRACTIONf_chiral_restr0.0656773
X-RAY DIFFRACTIONf_plane_restr0.0072885
X-RAY DIFFRACTIONf_dihedral_angle_d17.2431940

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