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- PDB-4gi5: Crystal Structure Of a Putative quinone reductase from Klebsiella... -

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Basic information

Entry
Database: PDB / ID: 4gi5
TitleCrystal Structure Of a Putative quinone reductase from Klebsiella pneumoniae (Target PSI-013613)
Componentsquinone reductase
KeywordsOXIDOREDUCTASE / Quinone reductase / Protein structure initiative / FAD bound / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) activity / nucleotide binding / cytosol
Similarity search - Function
: / Flavodoxin-like fold / Flavodoxin-like fold / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Unknown ligand / NAD(P)H dehydrogenase (Quinone)
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKumar, P.R. / Ahmed, M. / Banu, N. / Bhosle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Gizzi, A. / Glen, S. / Hammonds, J. ...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)
CitationJournal: to be published
Title: Crystal structure of a quinone reductase from Klebsiella pneumoniae with bound FAD
Authors: Kumar, P.R. / Hillerich, B. / Love, J. / Seidel, R. / Almo, S.C.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 20, 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: quinone reductase
B: quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,09214
Polymers63,9542
Non-polymers2,13812
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-78 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.834, 106.573, 109.326
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein quinone reductase / Putativae NAD(P)H dehydrogenase (Quinone)


Mass: 31976.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: KPN78578_46790, KPN_04757 / Plasmid: pSGC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6THR9

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Non-polymers , 5 types, 446 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.91 Å3/Da / Density % sol: 68.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M NA2HPO4/KH2PO4, PH 6.2, 2.5M NACL - MCSG3 #6); Cryoprotection (Glycerol), Sitting Drop, Vapor Diffusion, temperature ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M NA2HPO4/KH2PO4, PH 6.2, 2.5M NACL - MCSG3 #6); Cryoprotection (Glycerol), 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: Jun 14, 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: 1.75→50 Å / Num. obs: 194318 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.086 / Χ2: 1.542 / Net I/σ(I): 26.8979
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.75-1.785.90.8132.7596691.226100
1.78-1.815.90.70796861.244100
1.81-1.855.90.61297801.255100
1.85-1.895.90.50597101.311100
1.89-1.935.90.43697521.339100
1.93-1.975.90.34397231.342100
1.97-2.0260.2997131.361100
2.02-2.0760.2597221.393100
2.07-2.1460.20597991.402100
2.14-2.260.16897111.412100
2.2-2.2860.14396981.444100
2.28-2.3860.1397541.462100
2.38-2.4860.10797241.48100
2.48-2.6160.09597351.507100
2.61-2.7860.08597521.67100
2.78-2.9960.07896922.02100
2.99-3.295.90.06597672.393100
3.29-3.775.90.04697122.18699.8
3.77-4.755.80.03397101.7599.7
4.75-5060.03295091.65897.4

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-77.024-35.288-17.549S201
2-78.668-32.422-19.473S200.94
3-89.892-35.032-14.784S200.93
4-69.158-21.521-15.186S200.91
5-95.747-48.712-8.813S200.8
6-88.984-38.016-17.013S200.8
7-78.028-28.965-21.748S200.74
8-90.452-41.652-18.746S200.73
9-97.881-42.239-28.457S200.57
10-75.131-28.782-33.761S200.54
11-56.535-22.344-21.732S200.28
12-109.806-47.865-9.641S200.26
13-60.906-21.093-20.752S200.22
14-91.156-33.943-30.832S200.16
15-105.447-49.246-10.419S200.15
16-99.303-47.772-35.139S200.15
17-69.663-50.028-47.694S200.13
18-86.087-16.342-12.229S200.12
19-89.525-30.716-32.527S200.12
20-75.721-33.819-11.849S200.11
21-56.912-20.287-14.853S200.11
22-94.51-31.11-20.441S200.11
23-96.825-49.927-46.069S200.11
24-92.126-32.411-24.665S200.11
25-114.184-14.896-23.523S200.1
26-101.124-24.966-13.343S200.1
27-82.487-36.175-16.046S200.09
28-60.904-47.924-61.555S200.09
29-85.788-24.881-32.107S200.08
30-73.323-13.151-33.047S200.08
31-93.949-19.106-28.654S200.07
32-92.926-27.31-21.846S200.07
33-100.603-23.885-30.251S200.07
34-73.052-29.241-19.365S200.06
35-71.971-14.132-17.645S200.06
36-87.172-29.964-15.276S200.05
37-84.41-10.962-2.919S200.05
38-67.966-26.716-43.376S200.05
39-73.272-32.791-20.874S200.04

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→48.69 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1528 / WRfactor Rwork: 0.1358 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9201 / SU B: 1.271 / SU ML: 0.041 / SU R Cruickshank DPI: 0.064 / SU Rfree: 0.0649 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: A VERY LARGE POSITIVE DENSITY WAS SEEN ADJACENT TO THE FAD LIGANDS IN BOTH PROTEIN MONOMERS. THIS WAS INITIALLY MODELLED AS A BENZOIC ACID LIGAND (BEZ). THE EXACT IDENTITY OF THE ACTUAL ...Details: A VERY LARGE POSITIVE DENSITY WAS SEEN ADJACENT TO THE FAD LIGANDS IN BOTH PROTEIN MONOMERS. THIS WAS INITIALLY MODELLED AS A BENZOIC ACID LIGAND (BEZ). THE EXACT IDENTITY OF THE ACTUAL LIGAND IN THE STRUCTURE IS UNKNOWN. IT IS A POSSIBLE EXPRESSION ARTIFACT AND HAS BEEN DENOTED AS UNKNOWN LIGAND (UNL). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.163 5040 5 %RANDOM
Rwork0.144 ---
obs0.1449 101073 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.57 Å2 / Biso mean: 22.1059 Å2 / Biso min: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---1.23 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 157 434 4745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0194503
X-RAY DIFFRACTIONr_bond_other_d0.0010.024064
X-RAY DIFFRACTIONr_angle_refined_deg2.41.9786155
X-RAY DIFFRACTIONr_angle_other_deg1.04439332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69723.208212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.58715607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2881528
X-RAY DIFFRACTIONr_chiral_restr0.1570.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0215105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021129
LS refinement shellResolution: 1.752→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 352 -
Rwork0.21 6963 -
all-7315 -
obs--99.39 %

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