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- PDB-3mxl: Crystal structure of nitrososynthase from Micromonospora carbonac... -

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Basic information

Entry
Database: PDB / ID: 3mxl
TitleCrystal structure of nitrososynthase from Micromonospora carbonacea var. africana
ComponentsNitrososynthase
KeywordsOXIDOREDUCTASE / FLAVIN MONOOXYGENASE / NITROSOSYNTHASE / ACYL-COA DEHYDROGENASE
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 Å
AuthorsVey, J.L. / Iverson, T.M.
CitationJournal: Biochemistry / Year: 2010
Title: Structure and mechanism of ORF36, an amino sugar oxidizing enzyme in everninomicin biosynthesis .
Authors: Vey, J.L. / Al-Mestarihi, A. / Hu, Y. / Funk, M.A. / Bachmann, B.O. / Iverson, T.M.
History
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrososynthase
B: Nitrososynthase
C: Nitrososynthase
D: Nitrososynthase


Theoretical massNumber of molelcules
Total (without water)166,5104
Polymers166,5104
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-91 kcal/mol
Surface area57930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.815, 103.815, 295.954
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Nitrososynthase


Mass: 41627.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora carbonacea (bacteria) / Strain: var. africana / Gene: ORF36 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5APQ9

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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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M MgCl2, 10% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.2 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 6, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 29832 / Num. obs: 29783 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 111.2 Å2 / Rsym value: 0.116 / Net I/σ(I): 12.8
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.474 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.61 Å49.03 Å
Translation3.61 Å49.03 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
MD2software (EMBL)data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JIF

2jif


Resolution: 3.15→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2816 9.1 %Random
Rwork0.242 ---
all0.2457 31072 --
obs0.2457 29783 95.9 %-
Solvent computationBsol: 96.685 Å2
Displacement parametersBiso mean: 115.346 Å2
Baniso -1Baniso -2Baniso -3
1-0.901 Å20 Å20 Å2
2--0.901 Å20 Å2
3----1.802 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 3.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11016 0 0 0 11016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.14358
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.15→3.35 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.361 344 -
Rwork0.343 --
obs--86.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3cis_peptide.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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