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- PDB-3zoe: Crystal structure of FMN-binding protein (YP_005476) from Thermus... -

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Basic information

Entry
Database: PDB / ID: 3zoe
TitleCrystal structure of FMN-binding protein (YP_005476) from Thermus thermophilus with bound p-hydroxybenzaldehyde
ComponentsFLAVOREDOXIN
KeywordsFMN-BINDING PROTEIN
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / FMN binding
Similarity search - Function
: / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / P-HYDROXYBENZALDEHYDE / Flavoredoxin
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPavkov-Keller, T. / Steinkellner, G. / Gruber, C.C. / Steiner, K. / Winkler, C. / Schwamberger, O. / Schwab, H. / Faber, K. / Gruber, K.
CitationJournal: Nat.Commun. / Year: 2014
Title: Identification of Promiscuous Ene-Reductase Activity by Mining Structural Databases Using Active Site Constellations.
Authors: Steinkellner, G. / Gruber, C.C. / Pavkov-Keller, T. / Binter, A. / Steiner, K. / Winkler, C. / Lyskowski, A. / Schwamberger, O. / Oberer, M. / Schwab, H. / Faber, K. / Macheroux, P. / Gruber, K.
History
DepositionFeb 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: FLAVOREDOXIN
B: FLAVOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6406
Polymers39,4832
Non-polymers1,1574
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-51.7 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.660, 74.910, 77.590
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 FLAVOREDOXIN / FMN-BINDING PROTEIN


Mass: 19741.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB27 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q72HI0
#2: Chemical ChemComp-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: MORPHEUS SCREEN H5 10% W/V PEG 20 000, 20% V/V PEG MME 550; 0.02 M OF EACH AMINO ACID; 0.1 M MOPS/HEPES-NA PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Apr 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→37.5 Å / Num. obs: 39042 / % possible obs: 92.7 % / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.3 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USC

1usc


Resolution: 1.85→37.46 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.872 / SU B: 5.073 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27771 1308 5 %RANDOM
Rwork0.24196 ---
obs0.24381 24843 79.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--1.57 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 80 173 3009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192969
X-RAY DIFFRACTIONr_bond_other_d0.0010.022722
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9894048
X-RAY DIFFRACTIONr_angle_other_deg0.88636258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0135352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12121.791134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01615417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6051523
X-RAY DIFFRACTIONr_chiral_restr0.1060.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.542 71 -
Rwork0.521 1356 -
obs--59.76 %

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