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- PDB-3iup: Crystal structure of Putative NADPH:quinone oxidoreductase (YP_29... -

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Basic information

Entry
Database: PDB / ID: 3iup
TitleCrystal structure of Putative NADPH:quinone oxidoreductase (YP_296108.1) from RALSTONIA EUTROPHA JMP134 at 1.70 A resolution
ComponentsPutative NADPH:quinone oxidoreductase
KeywordsOXIDOREDUCTASE / YP_296108.1 / Putative NADPH:quinone oxidoreductase / 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
Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex ...Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-NDP / Possible NADH oxidoreductase
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative NADPH:quinone oxidoreductase (YP_296108.1) from RALSTONIA EUTROPHA JMP134 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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 20, 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 NADPH:quinone oxidoreductase
B: Putative NADPH:quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,60116
Polymers81,3742
Non-polymers2,22714
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-2 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.484, 77.927, 85.447
Angle α, β, γ (deg.)90.000, 109.210, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 2 - 376 / Label seq-ID: 3 - 377

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative NADPH:quinone oxidoreductase


Mass: 40687.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / Gene: Reut_A1899, YP_296108.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q470B9
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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.

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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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.2000M (NH4)2HPO4, 20.0000% PEG-3350, No Buffer pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97848,0.97790
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978481
30.97791
ReflectionResolution: 1.7→28.784 Å / Num. obs: 81898 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 25.768 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 10.55
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.5191.622770314289188.5
1.76-1.830.3672.23084715727196.3
1.83-1.910.2613.12983415212196.2
1.91-2.020.1694.73384317262196.5
2.02-2.140.1176.72933114960196.7
2.14-2.310.0819.23180716224196.3
2.31-2.540.06211.73045815546196.1
2.54-2.90.04415.53022115458195.9
2.9-3.660.02922.13049015653194.4
3.66-28.7840.02228.33007515476194.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.784 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 4.763 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.104
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. NADP WAS MODELED BASED ON STRUCTURAL HOMOLOGY AND DENSITY. THE OCCUPANCY IS SET TO 0.8 BASED ON DENSITY. 5. ACETATE (ACT) AND ETHYLENE GLYCOL (EDO) MODELED ARE PRESENT IN PURIFICATION BUFFER OR CRYO PROTECTANT.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 4102 5 %RANDOM
Rwork0.175 ---
obs0.176 81877 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.52 Å2 / Biso mean: 23.293 Å2 / Biso min: 10.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å2-0.13 Å2
2---0.01 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5477 0 144 618 6239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225938
X-RAY DIFFRACTIONr_bond_other_d0.0010.024001
X-RAY DIFFRACTIONr_angle_refined_deg1.6232.0018080
X-RAY DIFFRACTIONr_angle_other_deg1.10739833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5823.973219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02615994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5311539
X-RAY DIFFRACTIONr_chiral_restr0.0980.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021115
X-RAY DIFFRACTIONr_mcbond_it0.9041.53823
X-RAY DIFFRACTIONr_mcbond_other0.3081.51576
X-RAY DIFFRACTIONr_mcangle_it1.55626097
X-RAY DIFFRACTIONr_scbond_it2.39832115
X-RAY DIFFRACTIONr_scangle_it3.8284.51954
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2168MEDIUM POSITIONAL0.170.5
2276LOOSE POSITIONAL0.45
2168MEDIUM THERMAL1.282
2276LOOSE THERMAL1.1210
LS refinement shellResolution: 1.697→1.741 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 271 -
Rwork0.279 5509 -
all-5780 -
obs--94.23 %
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)
10.20950.1141-0.06231.29310.22330.24610.02460.01680.012-0.114-0.0394-0.04980.0077-0.03120.01480.0292-0.00140.00910.0311-0.00220.015420.052835.580617.2608
20.46720.06450.05031.06420.08080.20020.0167-0.0786-0.04780.0042-0.07250.0694-0.0165-0.00650.05590.0024-0.0017-0.00680.0460.00450.0262-5.058868.451425.9872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 377
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B2 - 376
4X-RAY DIFFRACTION2B401

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