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- PDB-3e39: Crystal structure of a putative nitroreductase in complex with fm... -

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Basic information

Entry
Database: PDB / ID: 3.0E+39
TitleCrystal structure of a putative nitroreductase in complex with fmn (dde_0787) from desulfovibrio desulfuricans subsp. at 1.70 A resolution
ComponentsPutative Nitroreductase
KeywordsOXIDOREDUCTASE / 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
ACETATE ION / FLAVIN MONONUCLEOTIDE / TRIETHYLENE GLYCOL / Nitroreductase
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans subsp. desulfuricans str. G20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Nitroreductase in Complex with FMN (YP_387283.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 Nitroreductase
B: Putative Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4488
Polymers39,2082
Non-polymers1,2406
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-47 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.780, 67.990, 99.740
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASN / End label comp-ID: PRO / Refine code: 6 / Auth seq-ID: 5 - 174 / Label seq-ID: 6 - 175

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsAUTHORS STATE THAT THE PROTOMER MAY FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS.

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Components

#1: Protein Putative Nitroreductase /


Mass: 19604.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans subsp. desulfuricans str. G20 (bacteria)
Gene: YP_387283.1, Dde_0787 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q314Q8
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE 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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 40.0000% PEG-400, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.918370,0.979421,0.979155
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2008 / Details: Vertical focusing mirror
RadiationMonochromator: Single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9794211
30.9791551
ReflectionResolution: 1.7→28.094 Å / Num. obs: 36111 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.566 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.760.4611.812636669499
1.76-1.830.3512.412888680598.7
1.83-1.910.2573.312508656498.5
1.91-2.020.1824.614055736797.9
2.02-2.140.1336.112162634997.2
2.14-2.310.1037.813285687096.8
2.31-2.540.091912857658396.6
2.54-2.90.06212.212735649295.9
2.9-3.660.03918.213090666494.8
3.66-28.0940.02923.913309651494

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.094 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.118 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.106
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. ACETATE AND PGE (PEG400 FRAGMENTS) WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 4. COFACTOR FMN WAS FOUND BOUND TO THE PROTEIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1806 5 %RANDOM
Rwork0.165 ---
obs0.166 36077 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.969 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 84 373 3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222854
X-RAY DIFFRACTIONr_bond_other_d0.0020.021911
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9983903
X-RAY DIFFRACTIONr_angle_other_deg0.98334652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1175363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.63323.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44115452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2541530
X-RAY DIFFRACTIONr_chiral_restr0.0970.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023187
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02557
X-RAY DIFFRACTIONr_nbd_refined0.2210.2581
X-RAY DIFFRACTIONr_nbd_other0.2160.22253
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21370
X-RAY DIFFRACTIONr_nbtor_other0.0870.21413
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.228
X-RAY DIFFRACTIONr_mcbond_it1.85631913
X-RAY DIFFRACTIONr_mcbond_other0.4783698
X-RAY DIFFRACTIONr_mcangle_it2.4452836
X-RAY DIFFRACTIONr_scbond_it3.76681225
X-RAY DIFFRACTIONr_scangle_it5.229111058
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2162 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.345
LOOSE THERMAL1.8710
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 134 -
Rwork0.218 2485 -
all-2619 -
obs--99.81 %

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