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- PDB-3pxv: Crystal structure of a Nitroreductase with bound FMN (Dhaf_2018) ... -

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Basic information

Entry
Database: PDB / ID: 3pxv
TitleCrystal structure of a Nitroreductase with bound FMN (Dhaf_2018) from Desulfitobacterium hafniense DCB-2 at 2.30 A resolution
ComponentsNitroreductase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / FMN-DEPENDENT / FMN-DEPENDENT NITROREDUCTASE-LIKE FOLD / 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
FLAVIN MONONUCLEOTIDE / Nitroreductase
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Nitroreductase with bound FMN (Dhaf_2018) from Desulfitobacterium hafniense DCB-2 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 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

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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
D: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3888
Polymers84,5634
Non-polymers1,8254
Water6,467359
1
A: Nitroreductase
B: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1944
Polymers42,2822
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-54 kcal/mol
Surface area15320 Å2
MethodPISA
2
C: Nitroreductase
D: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1944
Polymers42,2822
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-54 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.261, 81.577, 161.754
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
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A3 - 200
2112B3 - 200
3112C3 - 200
4112D3 - 200
DetailsCRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Nitroreductase /


Mass: 21140.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / DSM 10664 / Gene: Dhaf_2018, YP_002458491.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: B8FRE0
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 20.00% polyethylene glycol 3350, 0.20M ammonium dihydrogen phosphate, No Buffer pH 4.6, 0.001 M flavin mononucleotide (FMN), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97903
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.3→28.73 Å / Num. all: 36709 / Num. obs: 36709 / % possible obs: 99.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 34.74 Å2 / Rsym value: 0.143 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.363.60.6661.8934925930.66696.2
2.36-2.423.70.5962955026150.596100
2.42-2.493.70.5232.4945525380.52399.9
2.49-2.574.90.48631202624780.486100
2.57-2.664.80.4213.41165724060.421100
2.66-2.754.80.3593.81132223410.359100
2.75-2.854.90.3144.41086622300.314100
2.85-2.974.80.2465.31053621790.24699.9
2.97-3.14.80.1976.41008820830.19799.9
3.1-3.254.80.1468964919910.14699.9
3.25-3.434.80.1239.3927619200.12399.8
3.43-3.644.80.10510.8867617970.10599.8
3.64-3.894.80.09411.8824317020.09499.8
3.89-4.24.80.08312.8759515740.08399.6
4.2-4.64.80.07313.5705914750.07399.6
4.6-5.144.80.0813635313290.0899.2
5.14-5.944.70.09712.1562111840.09799.5
5.94-7.274.70.10411.6475610150.10498.9
7.27-10.294.50.07115.136538060.07198.4
10.29-28.734.20.0714.219074530.0794.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→28.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 13.135 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.233
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 SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.FLAVIN MONONUCLEOTIDE (FMN) ADDED AS AN ADDITIVE DURING CRYSTALLIZATION HAS BEEN MODELED BASED ON UNAMBIGUOUS ELECTRON DENSITY. 6.RESIDUES APPEARING AS RAMACHANDRAN OUTLIERS ARE IN A REGION OF ELECTRON DENSITY THAT IS NOT VERY WELL-DEFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1833 5 %RANDOM
Rwork0.1743 ---
obs0.1773 36660 99.57 %-
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: 110.16 Å2 / Biso mean: 51.0065 Å2 / Biso min: 20.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5694 0 124 359 6177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226000
X-RAY DIFFRACTIONr_bond_other_d0.0030.023980
X-RAY DIFFRACTIONr_angle_refined_deg1.5182.0058160
X-RAY DIFFRACTIONr_angle_other_deg0.94939761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1195770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41324.653245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5315991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8111531
X-RAY DIFFRACTIONr_chiral_restr0.0880.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216711
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021132
X-RAY DIFFRACTIONr_mcbond_it1.41733774
X-RAY DIFFRACTIONr_mcbond_other0.50431540
X-RAY DIFFRACTIONr_mcangle_it2.62656036
X-RAY DIFFRACTIONr_scbond_it4.66682226
X-RAY DIFFRACTIONr_scangle_it6.693112114
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1074TIGHT POSITIONAL0.180.05
B1074TIGHT POSITIONAL0.250.05
C1074TIGHT POSITIONAL0.320.05
D1074TIGHT POSITIONAL0.260.05
A1225MEDIUM POSITIONAL0.290.5
B1225MEDIUM POSITIONAL0.340.5
C1225MEDIUM POSITIONAL0.40.5
D1225MEDIUM POSITIONAL0.330.5
A1074TIGHT THERMAL0.780.5
B1074TIGHT THERMAL0.80.5
C1074TIGHT THERMAL0.80.5
D1074TIGHT THERMAL0.790.5
A1225MEDIUM THERMAL0.992
B1225MEDIUM THERMAL0.982
C1225MEDIUM THERMAL0.942
D1225MEDIUM THERMAL0.942
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 124 -
Rwork0.236 2528 -
all-2652 -
obs--98.92 %
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)
11.1918-0.27110.630.7606-0.34421.24250.02040.04990.0034-0.01210.01710.04-0.0735-0.0344-0.03750.00990.0040.00260.01310.00870.028732.84654.457690.0115
20.6225-0.2122-0.28660.8641-0.04031.8939-0.0118-0.0972-0.00030.1650.0159-0.13060.02740.0862-0.00410.0461-0.0097-0.04130.02420.01220.040444.081951.0805109.9845
31.0892-0.1649-0.42140.9336-0.19641.2491-0.0157-0.0464-0.01020.04620.01810.015-0.0049-0.0192-0.00240.01630.007-0.01640.0084-0.00880.0233-1.045526.883271.7685
40.51120.01990.26880.5882-0.29951.4978-0.00480.0990.1015-0.1211-0.003-0.1035-0.11520.28710.00780.0618-0.02580.0260.0702-0.00550.063610.50729.589751.9487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 200
2X-RAY DIFFRACTION2B0 - 200
3X-RAY DIFFRACTION3C1 - 200
4X-RAY DIFFRACTION4D0 - 200

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