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- PDB-1f8g: THE X-RAY STRUCTURE OF NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE F... -

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Basic information

Entry
Database: PDB / ID: 1f8g
TitleTHE X-RAY STRUCTURE OF NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE FROM RHODOSPIRILLUM RUBRUM COMPLEXED WITH NAD+
ComponentsNICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
KeywordsOXIDOREDUCTASE / Nucleotide fold / Proton pump Transhydrogenase / Rossmann fold
Function / homology
Function and homology information


NAD(P)+ transhydrogenase (Si-specific) activity / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADH binding / NADPH regeneration / NAD+ binding / NAD binding / NADP binding / protein dimerization activity / plasma membrane
Similarity search - Function
Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain ...Alanine dehydrogenase/NAD(P) transhydrogenase, conserved site-1 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(P) transhydrogenase subunit alpha part 1 / NAD(P) transhydrogenase subunit alpha part 1
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsBuckley, P.A. / Baz Jackson, J. / Schneider, T. / White, S.A. / Rice, D.W. / Baker, P.J.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Protein-protein recognition, hydride transfer and proton pumping in the transhydrogenase complex.
Authors: Buckley, P.A. / Baz Jackson, J. / Schneider, T. / White, S.A. / Rice, D.W. / Baker, P.J.
#1: Journal: To be Published
Title: The Crystallization of the dI Component of Transhydrogenase, A Proton-Translocating Membrane Protein
Authors: Sedelnikova, S.E. / Burke, J. / Buckley, P.A. / Rice, D.W. / Jackson, J.B. / Cotton, N.P.J. / Grindley, R.L. / Baker, P.J.
History
DepositionJun 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine
Item: _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct
Revision 1.4Oct 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_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: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
B: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
C: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
D: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7678
Polymers164,1134
Non-polymers2,6544
Water26,2841459
1
A: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
C: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3834
Polymers82,0562
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-31 kcal/mol
Surface area29820 Å2
MethodPISA
2
B: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
D: NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3834
Polymers82,0562
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-29 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.900, 116.600, 102.000
Angle α, β, γ (deg.)90.00, 104.22, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer. Two are present in asymmetric unit, chains A and C and chains B and D.

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Components

#1: Protein
NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE


Mass: 41028.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Plasmid: PCD1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q60164, UniProt: Q2RSB2*PLUS, NAD(P)+ transhydrogenase (Si-specific)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1459 / 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

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM NAD (+), 25% methylethyl PEG 2000, 200mM sodium phosphate buffer, pH7.5, 30mM Ammonium sulphate. , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Sedelnikova, S.E., (2000) Acta Crystallogr., D56, 1170.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-22 mg/mlprotein1drop
210 mMsodium phosphate1drop
330 mMammonium sulfate1drop
410 mMNAD+1drop
5200 mMsodium phosphate1reservoir
630 mMammonium sulfate1reservoir
710-20 %mPEG20001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM30A10.9796
SYNCHROTRONESRF BM30A20.9794
SYNCHROTRONESRF BM30A30.9686
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEOct 30, 1999
MARRESEARCH2IMAGE PLATEOct 30, 1999
MARRESEARCH3IMAGE PLATEOct 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97941
30.96861
ReflectionResolution: 2→20 Å / Num. all: 99140 / Num. obs: 99140 / % possible obs: 94.7 % / Redundancy: 3.22 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.271 / Num. unique all: 5966 / % possible all: 89.4
Reflection
*PLUS
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.26 4776 5% random
Rwork0.21 --
all-90649 -
obs-90649 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11116 0 158 1459 12733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d0.025
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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