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- PDB-2q6u: SeMet-substituted form of NikD -

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Basic information

Entry
Database: PDB / ID: 2q6u
TitleSeMet-substituted form of NikD
ComponentsNikD protein
KeywordsFLAVOPROTEIN / 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
BENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / NikD protein
Similarity search - Component
Biological speciesStreptomyces tendae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 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
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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)45,1593
Polymers44,2521
Non-polymers9082
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.520, 96.120, 78.050
Angle α, β, γ (deg.)90.00, 118.49, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer.

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Components

#1: Protein NikD protein


Mass: 44251.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces tendae (bacteria) / Strain: Tu501 / Gene: nikD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X9P9
#2: 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
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 30% PEG-1500, 50 mM HEPES, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9791, 0.9794, 0.9500, 1.0000
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.951
411
Reflection

D res high: 1.75 Å / D res low: 50 Å

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
115.13844550.0681.375103799.7
212.63766320.0731.295098799.6
311.13743390.071.035082399.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
3.775097.810.0541.898
2.993.7710010.0561.762
2.612.9910010.0671.66
2.382.6110010.0791.503
2.22.3810010.0911.399
2.072.210010.1031.282
1.972.0710010.131.181
1.891.9710010.1711.094
1.811.8910010.2260.995
1.751.8199.510.3040.902
3.775097.820.0541.664
2.993.7710020.0581.754
2.612.9910020.0741.699
2.382.6110020.0911.504
2.22.3810020.1061.346
2.072.210020.1211.203
1.972.0710020.1581.082
1.891.9710020.2080.94
1.811.8999.920.2750.83
1.751.819820.3660.754
3.775098.630.0491.324
2.993.7710030.0531.286
2.612.9910030.0691.179
2.382.6110030.091.074
2.22.3810030.1121.024
2.072.210030.1370.983
1.972.0710030.1870.929
1.891.9710030.2580.862
1.811.8999.530.3510.791
1.751.8194.730.4730.736
ReflectionResolution: 1.75→50 Å / Num. obs: 50708 / % possible obs: 99.3 % / Rmerge(I) obs: 0.07 / Χ2: 1.074 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.810.42548880.78795.7
1.81-1.890.31950510.85699.8
1.89-1.970.23950740.962100
1.97-2.070.17651171.065100
2.07-2.20.13150841.104100
2.2-2.380.10950911.113100
2.38-2.610.08751071.104100
2.61-2.990.06851181.158100
2.99-3.770.05551031.254100
3.77-500.05450751.23397.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
HKL-2000data reduction
XFITdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.75→20.11 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2501 4.9 %Random
Rwork0.191 ---
obs-49801 97.1 %-
Solvent computationBsol: 45.409 Å2
Displacement parametersBiso mean: 28.753 Å2
Baniso -1Baniso -2Baniso -3
1-0.337 Å20 Å24.468 Å2
2---1.182 Å20 Å2
3---0.845 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 62 252 3319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.0912.5
X-RAY DIFFRACTIONc_scbond_it3.483
X-RAY DIFFRACTIONc_mcangle_it33
X-RAY DIFFRACTIONc_scangle_it5.2344
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.07
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2fad_xplor.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4bez_xplor.param

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