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- PDB-3gag: Crystal structure of a nitroreductase-like protein (smu.346) from... -

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Basic information

Entry
Database: PDB / ID: 3gag
TitleCrystal structure of a nitroreductase-like protein (smu.346) from streptococcus mutans at 1.70 A resolution
ComponentsPutative NADH dehydrogenase, NADPH nitroreductase
KeywordsOXIDOREDUCTASE / Fmn-dependent nitroreductase-like fold / 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 / NADH dehydrogenase NAD(P)H nitroreductase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of nitroreductase-like protein (NP_720799.1) from Streptococcus mutans at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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 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
Revision 1.5Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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, NADPH nitroreductase
B: Putative NADH dehydrogenase, NADPH nitroreductase
C: Putative NADH dehydrogenase, NADPH nitroreductase
D: Putative NADH dehydrogenase, NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,74324
Polymers95,4364
Non-polymers3,30720
Water11,602644
1
A: Putative NADH dehydrogenase, NADPH nitroreductase
B: Putative NADH dehydrogenase, NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,46313
Polymers47,7182
Non-polymers1,74611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-43.8 kcal/mol
Surface area16990 Å2
MethodPISA
2
C: Putative NADH dehydrogenase, NADPH nitroreductase
D: Putative NADH dehydrogenase, NADPH nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,27911
Polymers47,7182
Non-polymers1,5619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-45.8 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.112, 52.478, 93.105
Angle α, β, γ (deg.)88.130, 80.350, 62.140
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 1 - 205 / Label seq-ID: 2 - 206

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsSTATIC LIGHT SCATTERING MEASUREMENTS INDICATE THAT A DIMER IS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Putative NADH dehydrogenase, NADPH nitroreductase


Mass: 23858.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: Clarke NCTC 10449 / Gene: NP_720799.1, SMU_346 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8DVW4
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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. THE STRAIN CLONED, STREPTOCOCCUS MUTANS CLARKE, DIFFERS FROM THE SEQUENCE DATABASE STRAIN, STREPTOCOCCUS MUTANS UA159. SEQUENCING OF THE CLONED CONSTRUCT SHOWS AN ARGININE AT POSITION 17 INSTEAD OF GLUTAMINE AND A GLYCINE AT POSITION 173 INSTEAD OF GLUTAMATE. THESE SUBSTITUTIONS ARE SUPPORTED BY THE ELECTRON DENSITY.

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: NANODROP, 0.160M (NH4)2SO4, 20.0% Glycerol, 20.0% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97953 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.7→29.591 Å / Num. obs: 81270 / % possible obs: 91.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 4.449
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.743.80.4711.61330035300.47153.4
1.74-1.793.80.3911.91578041780.39165.7
1.79-1.843.70.3352.21993953650.33585.9
1.84-1.940.2712.62330858940.27196.3
1.9-1.9640.2332.72239456450.23396.5
1.96-2.0340.1983.62195155240.19896.9
2.03-2.1140.1763.12116653450.17697.1
2.11-2.1940.1544.52022050990.15497.3
2.19-2.2940.13551961949600.13597.4
2.29-2.440.1325.11864047080.13297.7
2.4-2.533.90.1295.21769944820.12997.9
2.53-2.693.90.1165.71672742510.11698
2.69-2.873.90.1076.21591440540.10798.4
2.87-3.13.90.1026.31477937880.10298.7
3.1-3.43.90.0926.91327233990.09298.6
3.4-3.83.90.0797.81219631490.07998.9
3.8-4.393.90.0758.31079327830.07599.1
4.39-5.383.90.0768.1899323340.07699.3
5.38-7.63.70.0886.9674718060.08899.4
7.6-29.5913.70.0836.236319760.08397.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.591 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 4.202 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. A FLAVIN MONONUCLEOTIDE (FMN) IS MODELED IN EACH SUBUNIT. THE PLANARITY RESTRAINTS ON THE FMN ISOALLOXAZINE MOIETY WERE RELAXED TO ALLOW BUTTERFLY BENDING ALONG THE N5-N10 VIRTUAL AXIS TO BETTER FIT THE OBSERVED ELECTRON DENSITY. 5.SULFATE (SO4) AND GLYCEROL (GOL) MOLECULES FROM CRYSTALLIZATION SOLUTIONS ARE ALSO MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4057 5 %RANDOM
Rwork0.152 77212 --
obs0.154 81269 91.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 69.61 Å2 / Biso mean: 24.851 Å2 / Biso min: 10.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20.48 Å2-0.26 Å2
2---0.92 Å20.02 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6447 0 218 644 7309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227103
X-RAY DIFFRACTIONr_bond_other_d0.0020.024712
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9849685
X-RAY DIFFRACTIONr_angle_other_deg0.937311506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.485871
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1424.745333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.757151138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6171537
X-RAY DIFFRACTIONr_chiral_restr0.0980.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027971
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021402
X-RAY DIFFRACTIONr_nbd_refined0.2270.31704
X-RAY DIFFRACTIONr_nbd_other0.1970.35365
X-RAY DIFFRACTIONr_nbtor_refined0.1920.53551
X-RAY DIFFRACTIONr_nbtor_other0.0920.53395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.5946
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.10.53
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3180.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.326
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.531
X-RAY DIFFRACTIONr_mcbond_it1.1151.54411
X-RAY DIFFRACTIONr_mcbond_other0.2981.51698
X-RAY DIFFRACTIONr_mcangle_it1.50126888
X-RAY DIFFRACTIONr_scbond_it2.48833153
X-RAY DIFFRACTIONr_scangle_it3.6044.52797
Refine LS restraints NCS

Ens-ID: 1 / Number: 2367 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.220.5
2BMEDIUM POSITIONAL0.20.5
3CMEDIUM POSITIONAL0.250.5
4DMEDIUM POSITIONAL0.220.5
1AMEDIUM THERMAL0.782
2BMEDIUM THERMAL0.842
3CMEDIUM THERMAL0.812
4DMEDIUM THERMAL0.872
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 177 -
Rwork0.197 3352 -
all-3529 -
obs--53.36 %
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)
10.9041-0.3078-0.12231.90510.21491.29310.01290.07660.0834-0.1138-0.00810.0355-0.1817-0.1814-0.0047-0.03890.0476-0.0123-0.02490.002-0.066320.89727.350242.0591
21.0744-0.14-0.29850.59160.0220.6863-0.04560.075-0.0883-0.02660.0314-0.06550.0169-0.03980.0142-0.04880.0184-0.0075-0.0493-0.009-0.052128.1591-5.827741.2139
30.83030.268-0.18931.5974-0.34711.18580.0215-0.07030.08180.1094-0.03840.0102-0.14350.16580.0169-0.0506-0.0437-0.0127-0.0338-0.0039-0.064827.14632.503787.4217
41.35660.3291-0.23520.6143-0.07190.6226-0.0348-0.0512-0.10060.01280.02110.0540.02390.02530.0137-0.0598-0.0207-0.0083-0.06020.0063-0.045919.9021-10.647188.7096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 205
2X-RAY DIFFRACTION2B1 - 205
3X-RAY DIFFRACTION3C0 - 205
4X-RAY DIFFRACTION4D1 - 205

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