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- PDB-2oln: NikD, an unusual amino acid oxidase essential for nikkomycin bios... -

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Basic information

Entry
Database: PDB / ID: 2oln
TitleNikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: closed form at 1.15 A resolution
ComponentsnikD protein
KeywordsOXIDOREDUCTASE / flavoprotein / Rossmann fold
Function / homology
Function and homology information


flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDINE-2-CARBOXYLIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / NikD protein
Similarity search - Component
Biological speciesStreptomyces tendae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsCarrell, C.J. / Bruckner, R.C. / Venci, D. / Zhao, G. / Jorns, M.S. / Mathews, F.S.
CitationJournal: Structure / Year: 2007
Title: NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: structures of closed and open forms at 1.15 and 1.90 A resolution
Authors: Carrell, C.J. / Bruckner, R.C. / Venci, D. / Zhao, G. / Jorns, M.S. / Mathews, F.S.
History
DepositionJan 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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

Downloads & links

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Assembly

Deposited unit
A: nikD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1024
Polymers44,1701
Non-polymers9323
Water9,152508
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.24, 95.60, 77.90
Angle α, β, γ (deg.)90.00, 118.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-9431-

HOH

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Components

#1: Protein nikD protein


Mass: 44170.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: closed form / Source: (gene. exp.) Streptomyces tendae (bacteria) / Strain: Tu501 / Gene: nikD / Plasmid: pDV101 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X9P9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-6PC / PYRIDINE-2-CARBOXYLIC ACID / PICOLINIC ACID / Picolinic acid


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM ADA buffer, 28% PEG-1500, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Ge(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. all: 160538 / Num. obs: 160538 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.3
Reflection shellResolution: 1.15→1.17 Å / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 4.5 / % possible all: 46.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.15→50 Å / Num. parameters: 32357 / Num. restraintsaints: 39283 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1495 8054 5 %RANDOM
all0.1239 160511 --
obs0.1226 160511 90.1 %-
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 2901 / Occupancy sum non hydrogen: 3582.5
Refinement stepCycle: LAST / Resolution: 1.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 63 508 3595
Refine LS restraintsType: s_bond_d / Dev ideal: 0.017

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