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- PDB-4zyj: Streptomyces peucetius nitrososynthase dnmZ in TDP-bound state -

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Basic information

Entry
Database: PDB / ID: 4zyj
TitleStreptomyces peucetius nitrososynthase dnmZ in TDP-bound 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
THYMIDINE-5'-DIPHOSPHATE / Amino sugar nitrososynthase DnmZ
Similarity search - Component
Biological speciesStreptomyces peucetius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.736 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 Office of Research and Sponsored Projects 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 21, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,2518
Polymers181,6434
Non-polymers1,6094
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15530 Å2
ΔGint-122 kcal/mol
Surface area54840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.483, 134.667, 144.294
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
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA12 - 40532 - 425
21VALVALBB12 - 40532 - 425
12GLYGLYAA11 - 40531 - 425
22GLYGLYCC11 - 40531 - 425
13GLYGLYAA11 - 40531 - 425
23GLYGLYDD11 - 40531 - 425
14VALVALBB12 - 40532 - 425
24VALVALCC12 - 40532 - 425
15VALVALBB12 - 40532 - 425
25VALVALDD12 - 40532 - 425
16GLYGLYCC11 - 40531 - 425
26GLYGLYDD11 - 40531 - 425

NCS ensembles :
ID
1
2
3
4
5
6

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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: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 0.1 M glycine, 0.12 M ammonium sulfate, 12% PEG2000, pH 9.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.736→39.426 Å / Num. obs: 51414 / % possible obs: 98.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 74.36 Å2 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Rrim(I) all: 0.045 / Net I/σ(I): 32.9 / Num. measured all: 325167
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.736-2.8850.354.13366767040.170.354.188.9
2.88-3.066.90.2353.34931371360.0960.2357.699.9
3.06-3.276.70.1395.64518567200.0580.13912.799.9
3.27-3.536.40.0898.63983962560.0380.08919.999.8
3.53-3.876.60.05314.43796457870.0220.05332.999.8
3.87-4.336.20.033223221752340.0150.03347.499.7
4.33-56.70.02429.43140146790.010.02463.599.9
5-6.126.40.02330.92567039870.010.02360.299.9
6.12-8.656.30.01833.91944931110.0080.01876.199.8
8.65-39.4265.80.01243.81046218000.0050.012104.198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MXL

3mxl


Resolution: 2.736→39.426 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 2618 5.1 %RANDOM
Rwork0.1735 ---
obs0.1766 48689 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 183.62 Å2 / Biso mean: 61.685 Å2 / Biso min: 27.4 Å2
Refinement stepCycle: final / Resolution: 2.736→39.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11558 0 100 113 11771
Biso mean--94.65 50.7 -
Num. residues----1551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911838
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.98816073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3751537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11921.677495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.864151863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.88215148
X-RAY DIFFRACTIONr_chiral_restr0.1090.21861
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218964
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A4990.09
12B4990.09
21A5090.09
22C5090.09
31A5080.08
32D5080.08
41B4910.09
42C4910.09
51B4940.08
52D4940.08
61C5040.08
62D5040.08
LS refinement shellResolution: 2.736→2.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 123 -
Rwork0.273 2699 -
all-2822 -
obs--77.02 %

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