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- PDB-1hzz: THE ASYMMETRIC COMPLEX OF THE TWO NUCLEOTIDE-BINDING COMPONENTS (... -

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Basic information

Entry
Database: PDB / ID: 1hzz
TitleTHE ASYMMETRIC COMPLEX OF THE TWO NUCLEOTIDE-BINDING COMPONENTS (DI, DIII) OF PROTON-TRANSLOCATING TRANSHYDROGENASE
Components
  • PROTON-TRANSLOCATING NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT PNTAA
  • PROTON-TRANSLOCATING NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT PNTB
KeywordsOXIDOREDUCTASE / rossmann fold / alpha beta repeat / nucleotide-binding fold
Function / homology
Function and homology information


NAD(P)+ transhydrogenase (Si-specific) activity / proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADH binding / NAD+ binding / membrane => GO:0016020 / NAD binding / NADP binding / protein dimerization activity / plasma membrane
Similarity search - Function
NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / 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/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain ...NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / 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/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / 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 / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P) transhydrogenase subunit alpha part 1 / NAD(P) transhydrogenase subunit beta / NAD(P) transhydrogenase subunit beta / NAD(P) transhydrogenase subunit alpha part 1
Similarity search - Component
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsCotton, N.P.J. / White, S.A. / Peake, S.J. / McSweeney, S. / Jackson, J.B.
CitationJournal: Structure / Year: 2001
Title: The crystal structure of an asymmetric complex of the two nucleotide binding components of proton-translocating transhydrogenase.
Authors: Cotton, N.P. / White, S.A. / Peake, S.J. / McSweeney, S. / Jackson, J.B.
History
DepositionJan 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 21, 2021Group: Derived calculations / Refinement description / Category: refine / struct_site
Item: _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs ..._refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTON-TRANSLOCATING NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT PNTAA
B: PROTON-TRANSLOCATING NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT PNTAA
C: PROTON-TRANSLOCATING NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT PNTB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5425
Polymers102,1353
Non-polymers1,4072
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-44 kcal/mol
Surface area34830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.479, 74.166, 205.137
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTON-TRANSLOCATING NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT PNTAA


Mass: 40324.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: PNTAA / Production host: Escherichia coli (E. coli)
References: UniProt: Q60164, UniProt: Q2RSB2*PLUS, EC: 1.6.1.1
#2: Protein PROTON-TRANSLOCATING NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE SUBUNIT PNTB


Mass: 21485.510 Da / Num. of mol.: 1 / Fragment: RESIDUES 262-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: PNTB / Production host: Escherichia coli (E. coli)
References: UniProt: Q59765, UniProt: Q2RSB4*PLUS, EC: 1.6.1.1
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG-8K, ammonium sulphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMMES1reservoir
214-17 %PEG80001reservoir
3100-200 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97243 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 9, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 36218 / Num. obs: 135437 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 48.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4879 / % possible all: 88.1
Reflection
*PLUS
Num. obs: 36218 / Num. measured all: 135437
Reflection shell
*PLUS
% possible obs: 88.1 % / Num. unique obs: 4879 / Num. measured obs: 17745 / Rmerge(I) obs: 0.45

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→24.96 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 3075 4.8 %random
Rwork0.261 ---
all-64127 --
obs--95 %-
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.22 Å20 Å20 Å2
2--7.25 Å20 Å2
3----13.47 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å / Luzzati sigma a obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6669 0 92 74 6835
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.18
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.415 438 -
Rwork0.389 --
obs-9265 79.5 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.261
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 53.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.18
LS refinement shell
*PLUS
Rfactor Rfree: 0.415 / Rfactor Rwork: 0.389

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