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- PDB-5jv4: Structure of F420 binding protein, MSMEG_6526, from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 5jv4
TitleStructure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis with F420 bound
ComponentsPyridoxamine 5'-phosphate oxidase-like FMN-binding protein
KeywordsOXIDOREDUCTASE / Split beta-barrel / F420-dependent oxidoreductases / F420. / FMN-binding protein
Function / homology
Function and homology information


coenzyme F420 binding / oxidoreductase activity, acting on the CH-CH group of donors / cytosol
Similarity search - Function
F420-dependent enzyme, PPOX class, family Rv0121, probable / : / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
COENZYME F420 / Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein / Pyridoxamine 5'-phosphate oxidase family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLee, B.M. / Carr, P.D. / Jackson, C.J.
CitationJournal: To Be Published
Title: Structure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis with F420 bound
Authors: Lee, B.M. / Carr, P.D. / Jackson, C.J.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
B: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
C: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
D: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
E: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
F: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,74022
Polymers104,0126
Non-polymers5,72816
Water9,764542
1
A: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
D: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3596
Polymers34,6712
Non-polymers1,6884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-28 kcal/mol
Surface area13930 Å2
MethodPISA
2
B: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
E: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6908
Polymers34,6712
Non-polymers2,0206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-51 kcal/mol
Surface area14480 Å2
MethodPISA
3
C: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
F: Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6908
Polymers34,6712
Non-polymers2,0206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-37 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.951, 84.241, 75.980
Angle α, β, γ (deg.)90.00, 90.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-202-

MPD

21B-401-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Pyridoxamine 5'-phosphate oxidase-like FMN-binding protein


Mass: 17335.287 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: ERS451418_06325 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6J2M1, UniProt: A0R6F1*PLUS

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Non-polymers , 5 types, 558 molecules

#2: Chemical
ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C29H36N5O18P
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Sodium Acetate pH 4.6 20 mM Calcium Chloride 28% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9501 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9501 Å / Relative weight: 1
ReflectionResolution: 1.7→75.97 Å / Num. obs: 96899 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 6.6
Reflection shellResolution: 1.7→9.31 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZKY

4zky


Resolution: 1.7→75.97 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23081 4905 5.1 %RANDOM
Rwork0.1894 ---
obs0.1914 91915 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.502 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→75.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6544 0 276 542 7362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196599
X-RAY DIFFRACTIONr_bond_other_d00.026000
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9579096
X-RAY DIFFRACTIONr_angle_other_deg3.648313657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8255778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98622.733300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65415858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5151551
X-RAY DIFFRACTIONr_chiral_restr0.1750.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217389
X-RAY DIFFRACTIONr_gen_planes_other0.0220.021590
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_it2.0391.9283142
X-RAY DIFFRACTIONr_mcbond_other2.0391.9283141
X-RAY DIFFRACTIONr_mcangle_it3.012.8763910
X-RAY DIFFRACTIONr_mcangle_other3.012.8763911
X-RAY DIFFRACTIONr_scbond_it2.9472.3443450
X-RAY DIFFRACTIONr_scbond_other2.9472.3443451
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5533.3895179
X-RAY DIFFRACTIONr_long_range_B_refined6.50817.4298056
X-RAY DIFFRACTIONr_long_range_B_other6.37417.1437828
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 348 -
Rwork0.29 6750 -
obs--99.93 %

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