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- PDB-1nfp: STRUCTURAL REFINEMENT OF THE NON-FLUORESCENT FLAVOPROTEIN FROM PH... -

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Basic information

Entry
Database: PDB / ID: 1nfp
TitleSTRUCTURAL REFINEMENT OF THE NON-FLUORESCENT FLAVOPROTEIN FROM PHOTOBACTERIUM LEIOGNATHI AT 1.60 ANGSTROMS RESOLUTION
ComponentsLUXF GENE PRODUCT
KeywordsFLAVOPROTEIN / FLAVIN MONONUCLEOTIDE / MYRISTATE
Function / homology
Function and homology information


alkanal monooxygenase (FMN-linked) activity
Similarity search - Function
Bacterial luciferase, conserved site / Bacterial luciferase subunits signature. / Bacterial luciferase/NFP / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / MYRISTIC ACID / Non-fluorescent flavoprotein
Similarity search - Component
Biological speciesPhotobacterium leiognathi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsMoore, S.A. / Njames, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.60 A resolution.
Authors: Moore, S.A. / James, M.N.
#1: Journal: Protein Sci. / Year: 1994
Title: Common Structural Features of the Luxf Protein and the Subunits of Bacterial Luciferase: Evidence for a (Beta(Slash)Alpha)8 Fold in Luciferase
Authors: Moore, S.A. / James, M.N.G.
#2: Journal: Embo J. / Year: 1993
Title: Crystal Structure of a Flavoprotein Related to the Subunits of Bacterial Luciferase
Authors: Moore, S.A. / James, M.N.G. / O'Kane, D.J. / Lee, J.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization of Photobacterium Leiognathi Nfp, Non-Fluorescent Flavoprotein an Unusual Flavoprotein with Limited Sequence Identity to Bacterial Luciferase
Authors: Moore, S.A. / James, M.N.G. / O'Kane, D.J. / Lee, J.
History
DepositionFeb 27, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LUXF GENE PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7786
Polymers26,3131
Non-polymers1,4655
Water3,459192
1
A: LUXF GENE PRODUCT
hetero molecules

A: LUXF GENE PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,55612
Polymers52,6252
Non-polymers2,93110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9780 Å2
ΔGint-36 kcal/mol
Surface area19110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.930, 92.230, 99.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-423-

SO4

21A-307-

HOH

DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 1 1 .. 423 TWO-FOLD AXIS AT 0,Y,1/4: THE MOLECULE IS A SYMMETRICAL HOMODIMER. SYMMETRY1 1 -1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 49.66500

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Components

#1: Protein LUXF GENE PRODUCT


Mass: 26312.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium leiognathi (bacteria) / References: UniProt: P09142
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURAL FORMULA HYDROGEN ATOMS EQUIVALENTS PERTAIN TO THE OXIDIZED STATE OF FMN. THE ...THE STRUCTURAL FORMULA HYDROGEN ATOMS EQUIVALENTS PERTAIN TO THE OXIDIZED STATE OF FMN. THE CARBOXYLATE OF THE FATTY ACID IS IONIZED; IN ADDITION THE RIBOSE PHOSPHATE IS LIKELY SINGLY PROTONATED. THE PH OF THE CRYSTALS IS 5.5. THIS GIVES 43 HYDROGEN ATOMS FOR THE STRUCTURE, 8 ON THE ISOALLOXAZINE, 11 ON THE RIBOSE PHOSPHATE, AND 24 ON THE MYRISTATE. THE C3 OF THE FATTY ACID IS COVALENTLY LINKED TO C6 OF THE ISOALLOXAZINE NUCLEUS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.3 % / Description: DATA COLLECTED FROM TWO CRYSTALS
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
230-34 %satammonium sulfate1drop
350 mMsodium citrate1drop
43 %(w/v)isopropanol1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 1, 1992
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 28223 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 9999 Å / Num. measured all: 84138 / Rmerge(I) obs: 0.059 / Biso Wilson estimate: 16.07 Å2
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.67 Å / % possible obs: 65.6 % / Num. unique obs: 2590 / Num. measured obs: 3954

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Processing

Software
NameClassification
PROLSQrefinement
WEISdata reduction
RefinementResolution: 1.6→10 Å / σ(F): 1 /
RfactorNum. reflection% reflection
obs0.175 27451 78.7 %
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 99 192 2139
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.018
X-RAY DIFFRACTIONp_angle_d0.0360.032
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.036
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.052
X-RAY DIFFRACTIONp_mcangle_it3.13
X-RAY DIFFRACTIONp_scbond_it3.532.5
X-RAY DIFFRACTIONp_scangle_it5.563.7
X-RAY DIFFRACTIONp_plane_restr0.0140.018
X-RAY DIFFRACTIONp_chiral_restr0.1940.18
X-RAY DIFFRACTIONp_singtor_nbd0.2530.36
X-RAY DIFFRACTIONp_multtor_nbd0.1720.36
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2060.36
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor450
X-RAY DIFFRACTIONp_staggered_tor18.1100
X-RAY DIFFRACTIONp_orthonormal_tor24.3100
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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