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

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Basic information

Entry
Database: PDB / ID: 3zoh
TitleCrystal structure of FMN-binding protein (YP_005476) from Thermus thermophilus with bound 1-Cyclohex-2-enone
ComponentsFLAVOREDOXIN
KeywordsFMN-BINDING PROTEIN / CYCLOHEXENONE
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
cyclohex-2-en-1-one / FLAVIN MONONUCLEOTIDE / Flavoredoxin
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
C: FLAVOREDOXIN
D: FLAVOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,17612
Polymers78,9664
Non-polymers2,2108
Water11,169620
1
C: FLAVOREDOXIN
D: FLAVOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5886
Polymers39,4832
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-63.5 kcal/mol
Surface area13000 Å2
MethodPISA
2
A: FLAVOREDOXIN
B: FLAVOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5886
Polymers39,4832
Non-polymers1,1054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-59.7 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.771, 73.791, 77.374
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FLAVOREDOXIN


Mass: 19741.439 Da / Num. of mol.: 4
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-A2Q / cyclohex-2-en-1-one / cyclohex-2-enone


Mass: 96.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 12.5% PEG 1000, 12.5% W/V PEG 3350, 12.5% V/V MPD AND 0.1 M ACETATE BUFFER PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.505
11-h,-k,l20.495
ReflectionResolution: 1.65→30 Å / Num. obs: 86300 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / % possible all: 97

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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: 1.65→29.53 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.396 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18599 4235 4.9 %RANDOM
Rwork0.16111 ---
obs0.16236 81653 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.136 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å20 Å21.51 Å2
2--15.28 Å20 Å2
3----19.32 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5602 0 152 620 6374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196238
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9948528
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515755
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57722.332283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75315886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4531545
X-RAY DIFFRACTIONr_chiral_restr0.0780.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0225038
X-RAY DIFFRACTIONr_gen_planes_other
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: 1.648→1.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 278 -
Rwork0.275 5490 -
obs--90.83 %

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