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- PDB-2b67: Crystal structure of the Nitroreductase Family Protein from Strep... -

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Basic information

Entry
Database: PDB / ID: 2b67
TitleCrystal structure of the Nitroreductase Family Protein from Streptococcus pneumoniae TIGR4
ComponentsCOG0778: Nitroreductase
KeywordsOXIDOREDUCTASE / alpha-beta sandwich / FMN binding pocket / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
ACETIC ACID / FLAVIN MONONUCLEOTIDE / Nitroreductase family protein / Nitroreductase family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsKim, Y. / Volkart, L. / Abdullah, J. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Nitroreductase Family Protein from Streptococcus pneumoniae TIGR4
Authors: Kim, Y. / Volkart, L. / Abdullah, J. / Collart, F. / Joachimiak, A.
History
DepositionSep 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: COG0778: Nitroreductase
B: COG0778: Nitroreductase
C: COG0778: Nitroreductase
D: COG0778: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4059
Polymers92,5204
Non-polymers1,8855
Water13,565753
1
A: COG0778: Nitroreductase
B: COG0778: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2335
Polymers46,2602
Non-polymers9733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-46 kcal/mol
Surface area17550 Å2
MethodPISA
2
C: COG0778: Nitroreductase
D: COG0778: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1724
Polymers46,2602
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-48 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.400, 80.278, 103.015
Angle α, β, γ (deg.)90.00, 100.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
COG0778: Nitroreductase


Mass: 23129.896 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q97S03, UniProt: A0A0H2UP38*PLUS, NADH dehydrogenase
#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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 8000, MES, Calcium Acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2005 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.05→39.02 Å / Num. all: 56901 / Num. obs: 54339 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5056 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→39.02 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.038 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 5450 10 %RANDOM
Rwork0.17677 ---
all0.18378 48861 --
obs0.18378 48861 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.189 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0.22 Å2
2---0.7 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6388 0 128 753 7269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226776
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9969200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5585826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67124.448317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.299151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6041548
X-RAY DIFFRACTIONr_chiral_restr0.1020.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025096
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.23501
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24685
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2716
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9251.54216
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48426634
X-RAY DIFFRACTIONr_scbond_it2.2432992
X-RAY DIFFRACTIONr_scangle_it3.614.52566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 355 -
Rwork0.208 3308 -
obs-3308 89.3 %

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