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- PDB-4zky: Structure of F420 binding protein, MSMEG_6526, from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 4zky
TitleStructure of F420 binding protein, MSMEG_6526, from Mycobacterium smegmatis
ComponentsPyridoxamine 5-phosphate oxidase
KeywordsOXIDOREDUCTASE / MSMEG_6526 / F420 / FDR / FDOR / FDR-B / Reductase
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
IODIDE ION / Pyridoxamine 5'-phosphate oxidase family protein / :
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLee, B.M. / Carr, P.D. / Ahmed, F.H. / Jackson, C.J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Sequence-Structure-Function Classification of a Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria.
Authors: Ahmed, F.H. / Carr, P.D. / Lee, B.M. / Afriat-Jurnou, L. / Mohamed, A.E. / Hong, N.S. / Flanagan, J. / Taylor, M.C. / Greening, C. / Jackson, C.J.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxamine 5-phosphate oxidase
B: Pyridoxamine 5-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8655
Polymers31,6792
Non-polymers1853
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-40 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.704, 59.415, 95.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pyridoxamine 5-phosphate oxidase


Mass: 15839.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: L8F604, UniProt: A0R6F1*PLUS, pyridoxal 5'-phosphate synthase
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Sodium Iodide, 22% Peg 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→19.81 Å / Num. obs: 39312 / % possible obs: 98.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.3
Reflection shellResolution: 1.65→1.67 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 1.4 / % possible all: 76.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QVB

4qvb


Resolution: 1.65→19.396 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 1975 5.03 %
Rwork0.2223 39257 -
obs0.2242 39257 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→19.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 3 164 2357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072295
X-RAY DIFFRACTIONf_angle_d1.1143155
X-RAY DIFFRACTIONf_dihedral_angle_d12.088797
X-RAY DIFFRACTIONf_chiral_restr0.046353
X-RAY DIFFRACTIONf_plane_restr0.005412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6465-1.68760.36211050.32432145X-RAY DIFFRACTION80
1.6876-1.73320.39121280.3062608X-RAY DIFFRACTION98
1.7332-1.78420.37091220.29052672X-RAY DIFFRACTION99
1.7842-1.84180.31751340.26992661X-RAY DIFFRACTION100
1.8418-1.90750.30431370.25692700X-RAY DIFFRACTION100
1.9075-1.98380.28291440.24562652X-RAY DIFFRACTION100
1.9838-2.0740.28581400.24052673X-RAY DIFFRACTION100
2.074-2.18320.27781590.23382690X-RAY DIFFRACTION100
2.1832-2.31980.21921480.22712688X-RAY DIFFRACTION100
2.3198-2.49860.28651370.23712717X-RAY DIFFRACTION100
2.4986-2.74940.27281360.23452728X-RAY DIFFRACTION100
2.7494-3.14580.26961640.2272726X-RAY DIFFRACTION100
3.1458-3.95780.23721600.20182743X-RAY DIFFRACTION100
3.9578-19.39780.21641610.18452879X-RAY DIFFRACTION100

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