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- PDB-3bem: Crystal structure of putative nitroreductase ydfN (2632848) from ... -

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Basic information

Entry
Database: PDB / ID: 3bem
TitleCrystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution
ComponentsPutative NAD(P)H nitroreductase ydfN
KeywordsOXIDOREDUCTASE / 2632848 / putative nitroreductase ydfN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Flavoprotein / FMN / NAD / NADP
Function / homology
Function and homology information


Oxidoreductases / catabolic process / response to toxic substance / oxidoreductase activity / cytoplasm
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 / NICKEL (II) ION / S-1,2-PROPANEDIOL / Putative NAD(P)H nitroreductase MhqN
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Oct 30, 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
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. THE CONSTRUCT WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATIONS: RESIDUES LYS 147, GLU 148, AND LYS 149 WERE MUTATED TO ALA.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative NAD(P)H nitroreductase ydfN
B: Putative NAD(P)H nitroreductase ydfN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9678
Polymers50,7842
Non-polymers1,1836
Water6,035335
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.620, 69.200, 61.850
Angle α, β, γ (deg.)90.000, 100.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative NAD(P)H nitroreductase ydfN


Mass: 25392.166 Da / Num. of mol.: 2 / Mutation: K147A, E148A, K149A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: 2632848, ydfN, BSU05480 / Plasmid: MH4a / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: P96692, Oxidoreductases

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Non-polymers , 5 types, 341 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHH. ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHH. THE CONSTRUCT WAS ENGINEERED WITH THE REMARK 999 FOLLOWING MUTATIONS: RESIDUES LYS 147, GLU 148, AND LYS 149 REMARK 999 WERE MUTATED TO ALA.

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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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97939, 0.97953
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979391
30.979531
ReflectionResolution: 1.65→28.583 Å / Num. obs: 51334 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.797 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 8.98
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.65-1.710.2912.9168119336189.9
1.71-1.780.2363.61870810127197.2
1.78-1.860.1824.5180279778197.4
1.86-1.960.1445.51858510100197.8
1.96-2.080.1067178749721197.6
2.08-2.240.088.9182329972198.1
2.24-2.460.06211178129803198.1
2.46-2.820.05212.71817910152198
2.82-3.550.04315.41791110028198.4
3.55-28.5830.03617.9177859996197.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.65→28.583 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.982 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.083
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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. ACETATE AND 1,2-PROPANEDIOL WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. NI MODELED BASED ON GEOMETRY AND COORDINATION ENVIRONMENT. 6. FMN MODELED BASED ON DENSITY AND PROPOSED FUNCTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 2620 5.1 %RANDOM
Rwork0.151 ---
obs0.152 51310 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.4 Å2
2--0.09 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 77 335 3688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223599
X-RAY DIFFRACTIONr_bond_other_d0.0020.022390
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9754890
X-RAY DIFFRACTIONr_angle_other_deg0.99735851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58824.709172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86415638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7141521
X-RAY DIFFRACTIONr_chiral_restr0.0940.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024083
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02722
X-RAY DIFFRACTIONr_nbd_refined0.2280.2814
X-RAY DIFFRACTIONr_nbd_other0.20.22623
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21791
X-RAY DIFFRACTIONr_nbtor_other0.0880.21866
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2279
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.215
X-RAY DIFFRACTIONr_mcbond_it2.43332271
X-RAY DIFFRACTIONr_mcbond_other0.573880
X-RAY DIFFRACTIONr_mcangle_it3.06953530
X-RAY DIFFRACTIONr_scbond_it5.07881584
X-RAY DIFFRACTIONr_scangle_it7.211111356
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.207 179 -
Rwork0.178 3516 -
all-3695 -
obs--97.6 %
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)
10.33110.1480.21560.43660.22230.7819-0.02530.01160.0011-0.01240.0255-0.0219-0.04240.0689-0.00020.01510.01130.0014-0.0274-0.0026-0.0310.4188.8944.924
20.37440.30240.12940.54020.01710.94990.0279-0.0261-0.02240.0293-0.01310.02510.061-0.0869-0.01490.02190.00780.0004-0.0134-0.0049-0.0230.410.06849.839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 20612 - 218
2X-RAY DIFFRACTION2BB-3 - 2069 - 218

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