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- PDB-3kwk: Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitrored... -

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Basic information

Entry
Database: PDB / ID: 3kwk
TitleCrystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (NP_809094.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.54 A resolution
ComponentsPutative NADH dehydrogenase/NAD(P)H nitroreductase
KeywordsOXIDOREDUCTASE / Putative NADH dehydrogenase/NAD(P)H nitroreductase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Unknown ligand / Putative NADH dehydrogenase/NAD(P)H nitroreductase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative NADH dehydrogenase/NAD(P)H nitroreductase (NP_809094.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.54 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _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: Putative NADH dehydrogenase/NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3924
Polymers19,9001
Non-polymers4923
Water4,846269
1
A: Putative NADH dehydrogenase/NAD(P)H nitroreductase
hetero molecules

A: Putative NADH dehydrogenase/NAD(P)H nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7838
Polymers39,8002
Non-polymers9846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9080 Å2
ΔGint-66 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.215, 42.215, 186.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative NADH dehydrogenase/NAD(P)H nitroreductase


Mass: 19899.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_0181 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8ABC9
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE: THE CONSTRUCT (RESIDUES 26-199) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE: THE CONSTRUCT (RESIDUES 26-199) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M NaOAc, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97938
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 8, 2009
Details: Flat mirror, vertical and horizontal focussing mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 1.54→29.854 Å / Num. obs: 25905 / % possible obs: 98.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.54-1.583.10.551.4501316310.5587.5
1.58-1.623.50.5081.5620517590.50894.8
1.62-1.674.20.4421.8743817660.44299.4
1.67-1.725.30.3952921917320.395100
1.72-1.786.90.3532.21183217030.353100
1.78-1.847.10.2882.61171116580.288100
1.84-1.917.10.2233.41115915770.223100
1.91-1.997.10.1872.91088415330.187100
1.99-2.087.10.1622.71036114680.162100
2.08-2.187.10.1325.51004914250.132100
2.18-2.370.1255.6955013600.125100
2.3-2.4370.1166896712750.116100
2.43-2.670.1066.5857012280.106100
2.6-2.816.90.1066.2792811480.106100
2.81-3.086.90.1016722110490.101100
3.08-3.446.80.0797.866039640.079100
3.44-3.986.80.0639.859158760.063100
3.98-4.876.50.06210.148927490.062100
4.87-6.896.20.0689.237946160.068100
6.89-29.855.30.05810.120433880.05898.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.54→29.854 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.709 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.074
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. AN UNKNOWN LIGAND (UNL) WAS MODELED IN THE PUTATIVE ACTIVE SITE. CHLORIDE MODELED IS PRESENT IN CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 1313 5.1 %RANDOM
Rwork0.146 ---
obs0.147 25811 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.52 Å2 / Biso mean: 12.866 Å2 / Biso min: 2.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.54→29.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 34 269 1636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221505
X-RAY DIFFRACTIONr_bond_other_d0.0010.021044
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9942051
X-RAY DIFFRACTIONr_angle_other_deg0.91932547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.223.53865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5215268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8011511
X-RAY DIFFRACTIONr_chiral_restr0.0950.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211691
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02305
X-RAY DIFFRACTIONr_mcbond_it1.4543905
X-RAY DIFFRACTIONr_mcbond_other0.4393356
X-RAY DIFFRACTIONr_mcangle_it2.37951465
X-RAY DIFFRACTIONr_scbond_it4.2238600
X-RAY DIFFRACTIONr_scangle_it6.29711586
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 75 -
Rwork0.257 1554 -
all-1629 -
obs--86.74 %
Refinement TLS params.Method: refined / Origin x: 17.4788 Å / Origin y: 9.9865 Å / Origin z: 85.5659 Å
111213212223313233
T0.0111 Å20.0017 Å2-0.0017 Å2-0.0039 Å2-0.002 Å2--0.011 Å2
L0.3309 °2-0.0251 °2-0.1206 °2-0.3594 °20.0977 °2--0.5437 °2
S0.0011 Å °0.0258 Å °-0.001 Å °-0.0223 Å °0.0117 Å °-0.0348 Å °0.0275 Å °-0.0125 Å °-0.0128 Å °

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