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- PDB-3ha2: Crystal Structure of Protein (NADPH-quinone reductase) from P.pen... -

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Basic information

Entry
Database: PDB / ID: 3ha2
TitleCrystal Structure of Protein (NADPH-quinone reductase) from P.pentosaceus, Northeast Structural Genomics Consortium Target PtR24A
ComponentsNADPH-quinone reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics / Consortium / NESG / PtR24A / Northeast Structural Genomics Consortium / Flavoprotein
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) activity / FMN binding / electron transfer activity
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
DI(HYDROXYETHYL)ETHER / NADPH-quinone reductase
Similarity search - Component
Biological speciesPediococcus pentosaceus ATCC 25745 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target PtR24A
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 16, 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_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_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: NADPH-quinone reductase
B: NADPH-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4556
Polymers41,0612
Non-polymers3944
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-54 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.740, 65.740, 183.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein NADPH-quinone reductase


Mass: 20530.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus pentosaceus ATCC 25745 (bacteria)
Gene: PEPE_1665 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q03DN6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14% PEG4K 0.1M bis-tris 0.1M MgSO4, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2009 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 74707 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 65
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.7 / % possible all: 83.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.738 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22793 1786 5 %RANDOM
Rwork0.1979 ---
obs0.19941 33805 100 %-
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 mean: 28.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 21 152 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222793
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9483800
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0315336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47525.075134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39815455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.739158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022126
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21205
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21922
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8291.51733
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24722719
X-RAY DIFFRACTIONr_scbond_it2.37831216
X-RAY DIFFRACTIONr_scangle_it3.3174.51081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 94 -
Rwork0.208 1822 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 19.6063 Å / Origin y: 35.4724 Å / Origin z: 80.1051 Å
111213212223313233
T-0.0098 Å2-0.0456 Å2-0.016 Å2--0.1053 Å20.0031 Å2---0.0891 Å2
L1.0183 °2-0.3018 °2-0.1362 °2-1.0791 °2-0.0232 °2--0.9754 °2
S0.096 Å °-0.0214 Å °0.0597 Å °-0.1002 Å °-0.0408 Å °0.0315 Å °-0.1116 Å °0.0096 Å °-0.0551 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B180 - 249
2X-RAY DIFFRACTION1A180 - 261
3X-RAY DIFFRACTION1B178 - 179
4X-RAY DIFFRACTION1A178 - 179
5X-RAY DIFFRACTION1B1 - 168
6X-RAY DIFFRACTION1A1 - 168

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