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- PDB-3of4: Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreduct... -

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Basic information

Entry
Database: PDB / ID: 3of4
TitleCrystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreductase (nfnB, IL2077) from Idiomarina loihiensis L2TR at 1.90 A resolution
ComponentsNitroreductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / Unknown ligand / Nitroreductase
Similarity search - Component
Biological speciesIdiomarina loihiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a FMN/FAD- and NAD(P)H-dependent nitroreductase (nfnB, IL2077) from Idiomarina loihiensis L2TR at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitroreductase
B: Nitroreductase
C: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,12739
Polymers70,5513
Non-polymers4,57636
Water6,918384
1
A: Nitroreductase
B: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,69125
Polymers47,0342
Non-polymers2,65723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13200 Å2
ΔGint-122 kcal/mol
Surface area16640 Å2
MethodPISA
2
C: Nitroreductase
hetero molecules

C: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,87128
Polymers47,0342
Non-polymers3,83726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area12900 Å2
ΔGint-197 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.702, 74.051, 64.565
Angle α, β, γ (deg.)90.000, 112.490, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Nitroreductase


Mass: 23517.121 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Idiomarina loihiensis (bacteria) / Gene: nfnB, IL2077 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5R179

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Non-polymers , 7 types, 420 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.60M ammonium sulfate, 20.00% Glycerol, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97920,0.97889
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97921
30.978891
ReflectionResolution: 1.9→29.197 Å / Num. obs: 52053 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.96 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.76
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.3541.8111119387187.9
1.97-2.050.2382.6112079509189.9
2.05-2.140.1773.4106749100190.2
2.14-2.250.134.6108709270190.9
2.25-2.390.0956111079517191.3
2.39-2.580.0747.7115299942192.1
2.58-2.840.05110.7111839679193.1
2.84-3.250.03216.5112019754193.6
3.25-4.080.01927.5111009713194.1
4.08-29.1970.01434.8113689995194.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.197 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.576 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. ACETATE ION (ACT), GLYCEROL (GOL), AND SULFATE ION (SO4) ARE MODELED FROM THE CRYSTALLIZATION SOLUTION. 7. LIGAND MOLECULES FLAVIN-ADENINE DINUCLEOTIDE (FAD) AND FLAVIN MONONUCLEOTIDE (FMN) ARE MODELED BASED ON DENSITY. 8. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED NEAR FMN IN CHAINS A AND B. THE UNL RESEMBLES ADENINE MOIETY OF FAD AND OCCUPIES NCS RELATED EQUIVALENT POSITION OF THE SAME IN CHAIN C.
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 2638 5.1 %RANDOM
Rwork0.1574 ---
obs0.1592 52053 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 91.03 Å2 / Biso mean: 36.2008 Å2 / Biso min: 14.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å2-0.03 Å2
2---0.1 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4907 0 315 384 5606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225420
X-RAY DIFFRACTIONr_bond_other_d0.0010.023574
X-RAY DIFFRACTIONr_angle_refined_deg1.5252.0087388
X-RAY DIFFRACTIONr_angle_other_deg0.89938761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9515672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42324.802252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19215911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7321532
X-RAY DIFFRACTIONr_chiral_restr0.0840.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021044
X-RAY DIFFRACTIONr_mcbond_it0.7641.53189
X-RAY DIFFRACTIONr_mcbond_other0.2321.51287
X-RAY DIFFRACTIONr_mcangle_it1.32825153
X-RAY DIFFRACTIONr_scbond_it2.40932231
X-RAY DIFFRACTIONr_scangle_it3.5994.52208
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 197 -
Rwork0.225 3598 -
all-3795 -
obs--97.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.49720.274-0.12682.72930.89641.3419-0.08240.0064-0.13720.32540.147-0.06520.18890.1608-0.06460.07310.0554-0.00180.0895-0.02640.027249.326459.754223.1895
21.90720.0223-0.03472.09050.27322.1183-0.09970.1727-0.02420.04190.12890.23010.026-0.1502-0.02920.0234-0.00430.00830.0906-0.00720.038835.861966.17515.3016
31.109-0.2282-0.08681.21470.42812.4747-0.0875-0.00630.0621-0.0326-0.06910.0821-0.1011-0.14580.15660.02060.0114-0.0230.0119-0.0160.096444.417726.334159.5382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 208
2X-RAY DIFFRACTION2B1 - 208
3X-RAY DIFFRACTION3C1 - 208

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