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- PDB-1pnq: Crystal structure of R. rubrum transhydrogenase domain III bound ... -

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Basic information

Entry
Database: PDB / ID: 1pnq
TitleCrystal structure of R. rubrum transhydrogenase domain III bound to NADPH
ComponentsNAD(P) transhydrogenase subunit beta
KeywordsOXIDOREDUCTASE / Nucleotide binding fold / NADPH
Function / homology
Function and homology information


proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / membrane => GO:0016020 / NADP binding / plasma membrane
Similarity search - Function
NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / NAD(P) transhydrogenase subunit beta / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSundaresan, V. / Yamaguchi, M. / Chartron, J. / Stout, C.D.
CitationJournal: Biochemistry / Year: 2003
Title: Conformational Change in the NADP(H) Binding Domain of Transhydrogenase Defines Four States
Authors: Sundaresan, V. / Yamaguchi, M. / Chartron, J. / Stout, C.D.
History
DepositionJun 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD(P) transhydrogenase subunit beta
B: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3754
Polymers38,8842
Non-polymers1,4912
Water2,972165
1
A: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1882
Polymers19,4421
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1882
Polymers19,4421
Non-polymers7451
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.270, 118.270, 212.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-122-

HOH

21B-73-

HOH

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Components

#1: Protein NAD(P) transhydrogenase subunit beta / Pyridine nucleotide transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase ...Pyridine nucleotide transhydrogenase subunit beta / Nicotinamide nucleotide transhydrogenase subunit beta / Proton-translocating transhydrogenase NADP(H)-binding component / dIII


Mass: 19442.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q59765, UniProt: Q2RSB4*PLUS, EC: 1.6.1.2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulfate, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Temperature: 8 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris-HCl1droppH8.2
20.8 mMdithiothreitol1drop
30.4 mMPMSF1drop
41 mMNADPH1drop
514 mg/mlprotein1drop
60.6 Mammonium sulfate1reservoir
730 mMsodium citrate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→19.65 Å / Num. obs: 34800 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 9.1 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.085 / Net I/σ(I): 17.3
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.1 % / Num. unique all: 2367 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 19.7 Å / Num. measured all: 317639 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.63 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2344125.44 / Data cutoff high rms absF: 2344125.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1716 4.9 %RANDOM
Rwork0.215 ---
all0.216 35062 --
obs0.215 34733 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.751 Å2 / ksol: 0.342248 e/Å3
Displacement parametersBiso mean: 58.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 96 166 2960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 261 4.8 %
Rwork0.34 5144 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NADPH.PARAMNADPH.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 19.7 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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