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- PDB-4zxv: Streptomyces peucetius nitrososynthase DnmZ in ligand-free state -

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Basic information

Entry
Database: PDB / ID: 4zxv
TitleStreptomyces peucetius nitrososynthase DnmZ in ligand-free state
ComponentsDnmZ
KeywordsOXIDOREDUCTASE / nitrososynthase / flavin monooxygenase / aminosugar / cis-peptide / acyl-coA dehydrogenase / flavin
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on the CH-CH group of donors / antibiotic biosynthetic process / monooxygenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain ...Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / 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
Amino sugar nitrososynthase DnmZ
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSartor, L.M. / Vey, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
CSU Program for Education and Research in Biotechnology United States
CSUN Research and Grants Committee Mini-Grant United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5SC2AI109500 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structure of DnmZ, a nitrososynthase in the Streptomyces peucetius anthracycline biosynthetic pathway.
Authors: Sartor, L. / Ibarra, C. / Al-Mestarihi, A. / Bachmann, B.O. / Vey, J.L.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: DnmZ
B: DnmZ
C: DnmZ
D: DnmZ


Theoretical massNumber of molelcules
Total (without water)181,6434
Polymers181,6434
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.836, 134.491, 142.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A10 - 188
2111B10 - 188
3111C10 - 188
4111D10 - 188
1211A196 - 405
2211B196 - 405
3211C196 - 405
4211D196 - 405
1124A189 - 195
2124B189 - 195
3124D189 - 195

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.324633, -0.073592, -0.942973), (-0.06643, -0.992733, 0.100345), (-0.943504, 0.095217, 0.317385)-53.124741, 12.33933, -38.87159
3given(-0.999608, 0.027805, 0.00329), (0.027116, 0.990645, -0.133746), (-0.006978, -0.133604, -0.99101)-77.324387, 0.77048, -5.13871
4given(0.346557, 0.021837, 0.937775), (0.018005, -0.9997, 0.016626), (0.937856, 0.011123, -0.346846)-22.285669, 15.33125, 32.403141
5given(1), (1), (1)
6given(-0.397714, -0.315608, -0.861519), (0.168428, -0.948133, 0.269585), (-0.901918, -0.037886, 0.430243)-47.80933, 31.399851, -28.78903
7given(0.328516, -0.154532, 0.931771), (0.059336, -0.981199, -0.18365), (0.942633, 0.115619, -0.313171)-17.23576, 21.533501, 28.518881

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Components

#1: Protein
DnmZ


Mass: 45410.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces peucetius (bacteria) / Gene: dnmZ / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0R4I990*PLUS, EC: 1.14.13.187
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.3
Details: 0.1 M glycine, 0.12 M ammonium sulfate, 12% PEG2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 38251 / % possible obs: 97.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 97.065 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.054 / Net I/σ(I): 17.5 / Num. measured all: 123512
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3-3.113.10.4652.336910.90195.3
3.11-3.233.30.34937790.99698.8
3.23-3.383.30.25437931.07798.4
3.38-3.563.10.18237901.22297.4
3.56-3.783.40.13438031.20898.7
3.78-4.073.30.10338371.20798.8
4.07-4.483.10.0837851.05397.1
4.48-5.133.30.06938701.00198.7
5.13-6.463.20.05638971.03198.1
6.46-503.20.02740060.83496.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.84 Å39.35 Å
Translation2.84 Å39.35 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.1.4phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
Blu-Icedata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MXL

3mxl


Resolution: 3→48.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1937 5.1 %RANDOM
Rwork0.2102 ---
obs0.2131 36262 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 223.18 Å2 / Biso mean: 100.166 Å2 / Biso min: 42.12 Å2
Refinement stepCycle: final / Resolution: 3→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11438 0 0 27 11465
Biso mean---76.03 -
Num. residues----1571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911624
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.97515816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.32451562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21822.088455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.618151741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.80115122
X-RAY DIFFRACTIONr_chiral_restr0.0890.21867
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218838
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2722TIGHT THERMAL14.940.5
12B2722TIGHT THERMAL17.860.5
13C2722TIGHT THERMAL10.520.5
14D2722TIGHT THERMAL11.740.5
21A14MEDIUM POSITIONAL0.290.5
22B14MEDIUM POSITIONAL0.520.5
23D14MEDIUM POSITIONAL0.340.5
21A14MEDIUM THERMAL11.252
22B14MEDIUM THERMAL5.092
23D14MEDIUM THERMAL8.92
LS refinement shellResolution: 3.003→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 117 -
Rwork0.29 2357 -
all-2474 -
obs--92.52 %

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