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- PDB-4fek: Crystal Structure of putative diflavin flavoprotein A 5 (fragment... -

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Basic information

Entry
Database: PDB / ID: 4fek
TitleCrystal Structure of putative diflavin flavoprotein A 5 (fragment 1-254) from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR435A , Northeast Structural Genomics Consortium (NESG) Target NsR435A
ComponentsPutative diflavin flavoprotein A 5
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / dfa5 / all0177
Function / homology
Function and homology information


Oxidoreductases / FMN binding / electron transfer activity
Similarity search - Function
Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Flavodoxin, conserved site / Flavodoxin signature. / FMN-binding split barrel / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase ...Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / Flavodoxin, conserved site / Flavodoxin signature. / FMN-binding split barrel / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Putative diflavin flavoprotein A 5
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKuzin, A. / Abashidze, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. ...Kuzin, A. / Abashidze, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target NsR435A
Authors: Kuzin, A. / Abashidze, M. / Seetharaman, J. / Janjua, J. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 30, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJul 11, 2012ID: 3HNN
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / database_2 / pdbx_initial_refinement_model / 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 / _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
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative diflavin flavoprotein A 5
B: Putative diflavin flavoprotein A 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3657
Polymers59,9272
Non-polymers4385
Water3,315184
1
A: Putative diflavin flavoprotein A 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2004
Polymers29,9641
Non-polymers2373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative diflavin flavoprotein A 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1653
Polymers29,9641
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.651, 57.993, 106.606
Angle α, β, γ (deg.)90.00, 102.42, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer,31.78 kD,93.8%

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Components

#1: Protein Putative diflavin flavoprotein A 5


Mass: 29963.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 (bacteria) / Gene: dfa5, all0177 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q8Z0C1, Oxidoreductases
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl, pH 7.5. Reservoir solution:0.1 M KH2PO4, 0.1 M Tris HCL, 18% PEG3350,, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 79297 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 28.8

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Processing

Software
NameVersionClassificationNB
PHENIXdev_988refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HNN

3hnn
PDB Unreleased entry


Resolution: 2→28.373 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 2038 5.01 %
Rwork0.2091 --
obs0.2107 40681 99.14 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.612 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3453 Å20 Å2-5.2653 Å2
2--6.6434 Å2-0 Å2
3----2.298 Å2
Refinement stepCycle: LAST / Resolution: 2→28.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3987 0 25 184 4196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084116
X-RAY DIFFRACTIONf_angle_d1.1665590
X-RAY DIFFRACTIONf_dihedral_angle_d13.3271527
X-RAY DIFFRACTIONf_chiral_restr0.078630
X-RAY DIFFRACTIONf_plane_restr0.005710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0004-2.04690.26321280.20852552X-RAY DIFFRACTION99
2.0469-2.0980.23271280.22712574X-RAY DIFFRACTION99
2.098-2.15480.33491300.21342585X-RAY DIFFRACTION100
2.1548-2.21810.23981230.22012587X-RAY DIFFRACTION100
2.2181-2.28970.30391340.26412476X-RAY DIFFRACTION95
2.2897-2.37150.24921370.22192557X-RAY DIFFRACTION100
2.3715-2.46640.25141240.20942601X-RAY DIFFRACTION100
2.4664-2.57860.28151390.22242586X-RAY DIFFRACTION100
2.5786-2.71440.33051400.23042592X-RAY DIFFRACTION100
2.7144-2.88430.25251350.23212593X-RAY DIFFRACTION100
2.8843-3.10680.27941260.2272611X-RAY DIFFRACTION100
3.1068-3.4190.25991760.20562576X-RAY DIFFRACTION100
3.419-3.91260.22361440.20042605X-RAY DIFFRACTION100
3.9126-4.92530.16971400.16782606X-RAY DIFFRACTION99
4.9253-28.37630.20641340.20632542X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 9.3467 Å / Origin y: 23.9466 Å / Origin z: 75.895 Å
111213212223313233
T0.1708 Å2-0.0696 Å20.0632 Å2-0.0631 Å20.0437 Å2--0.1664 Å2
L4.3336 °2-0.2409 °22.8653 °2-0.5188 °2-0.3999 °2--3.2446 °2
S0.1839 Å °-0.6062 Å °-0.2237 Å °0.2201 Å °0.0422 Å °-0.0472 Å °0.118 Å °-0.096 Å °0.0264 Å °
Refinement TLS groupSelection details: all

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