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- PDB-3pft: Crystal Structure of Untagged C54A Mutant Flavin Reductase (DszD)... -

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Basic information

Entry
Database: PDB / ID: 3pft
TitleCrystal Structure of Untagged C54A Mutant Flavin Reductase (DszD) in Complex with FMN From Mycobacterium goodii
ComponentsFlavin reductase
KeywordsOXIDOREDUCTASE / Flavin Reductase / Desulfurization
Function / homology
Function and homology information


FMN reductase (NADH) / FAD reductase (NADH) / dibenzothiophene catabolic process / riboflavin reductase (NADPH) activity / FMN binding / cytoplasm
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 / NADH:FMN oxidoreductase
Similarity search - Component
Biological speciesMycobacterium goodii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsLi, Q. / Xu, P. / Ma, C. / Gu, L. / Liu, X. / Zhang, C. / Li, N. / Su, J. / Li, B. / Liu, S.
CitationJournal: To be Published
Title: The flavin reductase DSZD from a desulfurizing mycobacterium goodii strain: systemic manipulation and investigation based on the crystal structure
Authors: Li, Q. / Xu, P. / Ma, C. / Gu, L. / Liu, X. / Zhang, C. / Li, N. / Su, J. / Li, B. / Liu, S.
History
DepositionOct 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Flavin reductase
B: Flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8584
Polymers32,9452
Non-polymers9132
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-46 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.174, 131.174, 131.174
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-250-

HOH

21B-307-

HOH

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Components

#1: Protein Flavin reductase


Mass: 16472.627 Da / Num. of mol.: 2 / Fragment: UNP residues 5-161 / Mutation: C54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium goodii (bacteria) / Strain: X7B / Gene: dszD / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6CDL6, EC: 1.5.1.29
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.85 Å3/Da / Density % sol: 56.91 % / Mosaicity: 0.263 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 34% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 49333 / % possible obs: 99.9 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.059 / Χ2: 1.204 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6514.10.59344250.8271100
1.65-1.7114.70.45844620.8181100
1.71-1.7814.90.32644400.8761100
1.78-1.8615.10.2544690.9041100
1.86-1.9615.30.18544851.1621100
1.96-2.0815.60.11444530.9811100
2.08-2.2415.80.0844610.8681100
2.24-2.4715.80.07345131.1871100
2.47-2.8215.60.07744822.1991100
2.82-3.5615.60.05245272.1521100
3.56-5015.20.02846161.157199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→35.058 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8869 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2375 5.03 %RANDOM
Rwork0.1732 ---
obs0.1743 47171 95.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.609 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 69.47 Å2 / Biso mean: 23.5352 Å2 / Biso min: 9.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.601→35.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 62 440 2823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092508
X-RAY DIFFRACTIONf_angle_d1.1943458
X-RAY DIFFRACTIONf_chiral_restr0.076410
X-RAY DIFFRACTIONf_plane_restr0.01438
X-RAY DIFFRACTIONf_dihedral_angle_d17.934906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6009-1.63350.27451470.21132456260391
1.6335-1.66910.24571480.19962486263492
1.6691-1.70790.24061330.19022506263992
1.7079-1.75060.21871140.18982565267993
1.7506-1.79790.24481380.18482572271093
1.7979-1.85080.22321390.18732525266493
1.8508-1.91060.21711380.17742582272093
1.9106-1.97890.21511520.17992574272696
1.9789-2.05810.19791250.17262697282296
2.0581-2.15170.19291310.17292696282798
2.1517-2.26520.17191400.16812706284698
2.2652-2.4070.19211460.16982650279697
2.407-2.59280.19471430.17462683282697
2.5928-2.85370.18751470.1762738288598
2.8537-3.26630.21161490.16732712286198
3.2663-4.11420.15981460.155327822928100
4.1142-35.06610.17911390.1642866300599

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