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- PDB-4g8s: Crystal Structure Of a Putative Nitroreductase from Geobacter sul... -

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Basic information

Entry
Database: PDB / ID: 4g8s
TitleCrystal Structure Of a Putative Nitroreductase from Geobacter sulfurreducens PCA (Target PSI-013445)
ComponentsNitroreductase family protein
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium (NYSGRC)
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-like family 3 protein
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsKumar, P.R. / Bhosle, R. / Hillerich, B. / Seidel, R. / Toro, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: to be published
Title: Crystal structure of a nitroreductase from Geobacter sulfurreducens PCA
Authors: Kumar, P.R. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. / Hillerich, B. / Love, J.D. / Seidel, R. / Stead, M. / ...Authors: Kumar, P.R. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. / Hillerich, B. / Love, J.D. / Seidel, R. / Stead, M. / Toro, R. / Washington, E. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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: Nitroreductase family protein
B: Nitroreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8565
Polymers46,8512
Non-polymers1,0053
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-32 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.759, 73.759, 169.472
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a dimer

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Components

#1: Protein Nitroreductase family protein


Mass: 23425.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA, ATCC 51573 / Gene: GSU0217 / Plasmid: pSGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q74GM9
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (0.2M Potassium Chloride, 20% PEG 3350 - MCSG1 #89), Cryoprotection (Ethylene glycol), Sitting Drop, Vapor Diffusion, ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol, Reservoir (0.2M Potassium Chloride, 20% PEG 3350 - MCSG1 #89), Cryoprotection (Ethylene glycol), Sitting Drop, Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 45382 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 35.58 Å2 / Rmerge(I) obs: 0.097 / Χ2: 2.21 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.2412.70.79122671.3461100
2.24-2.2812.70.66222291.4491100
2.28-2.3212.70.59323191.4381100
2.32-2.3712.80.52522601.4481100
2.37-2.4212.70.44922731.4641100
2.42-2.4812.80.40522341.4821100
2.48-2.5412.80.32823201.5421100
2.54-2.6112.80.26522371.6231100
2.61-2.6912.80.24322571.7021100
2.69-2.7712.70.19222711.841100
2.77-2.8712.70.17322531.8981100
2.87-2.9912.60.1522962.0551100
2.99-3.1212.50.12322602.3581100
3.12-3.2912.30.10222702.6421100
3.29-3.4911.90.08422843.1541100
3.49-3.7611.40.07322483.51100
3.76-4.1411.10.06422843.7141100
4.14-4.7411.10.05422723.7591100
4.74-5.9711.50.05122703.4771100
5.97-5012.10.0422783.146199.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
DENZOdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→36.738 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8825 / SU ML: 0.16 / σ(F): 0 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1971 1990 8.15 %RANDOM
Rwork0.1623 ---
obs0.1651 24421 99.4 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.78 Å2 / Biso mean: 31.9928 Å2 / Biso min: 10.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 68 109 2974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082939
X-RAY DIFFRACTIONf_angle_d1.0293993
X-RAY DIFFRACTIONf_chiral_restr0.066437
X-RAY DIFFRACTIONf_plane_restr0.005515
X-RAY DIFFRACTIONf_dihedral_angle_d13.4941088
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2002-2.25520.22271340.19081545167998
2.2552-2.31620.24931390.17991555169498
2.3162-2.38430.20191400.17551561170199
2.3843-2.46130.23461390.16761566170599
2.4613-2.54920.20231390.1661553169299
2.5492-2.65130.22261400.160315781718100
2.6513-2.77190.19511400.163815811721100
2.7719-2.9180.21321430.170216011744100
2.918-3.10070.24821410.174815911732100
3.1007-3.340.20781420.178516111753100
3.34-3.67580.17791440.149916231767100
3.6758-4.20710.16981450.1416301775100
4.2071-5.29790.16281490.138616701819100
5.2979-36.74350.20481550.18491766192199
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)
11.76230.43010.22.42910.39351.1024-0.0466-0.09860.05030.18480.0770.2353-0.1085-0.0895-0.02340.29760.0027-0.03310.0565-0.00290.215723.14857.363665.8817
21.58090.11460.01861.6776-0.45580.1256-0.08820.1199-0.17710.1587-0.02360.1080.3485-0.035-0.02660.3269-0.0226-0.03810.0666-0.01430.173730.95996.569859.4582
30.669-0.25680.09881.5495-0.06560.467-0.01390.12470.063-0.2626-0.02290.3155-0.0298-0.0165-0.06350.3103-0.0307-0.04910.07280.03260.231118.31695.715858.3476
42.2562-0.19840.22531.90960.36452.1119-0.04890.3140.1741-0.1250.0371-0.2756-0.31160.526-0.06770.2528-0.0974-0.03640.228-0.00040.21945.94189.750654.3674
53.29210.2434-0.15781.67040.34191.7751-0.27280.331-0.0177-0.40890.33640.0243-0.04480.22130.06150.3304-0.0286-0.05420.11960.00460.131937.65976.054858.5949
63.10220.21530.00533.6406-0.10062.8593-0.06980.1191-0.1734-0.11370.0435-0.46470.17170.62240.05350.18240.0188-0.01270.2467-0.06420.208849.03222.18257.6976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:98)A1 - 98
2X-RAY DIFFRACTION2chain 'A' and (resseq 99:133)A99 - 133
3X-RAY DIFFRACTION3chain 'A' and (resseq 134:187)A134 - 187
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:98)B1 - 98
5X-RAY DIFFRACTION5chain 'B' and (resseq 99:133)B99 - 133
6X-RAY DIFFRACTION6chain 'B' and (resseq 134:186)B134 - 186

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