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- PDB-4izh: Crystal Structure of the Alpha1 dimer of Thermus thermophilus Tra... -

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Basic information

Entry
Database: PDB / ID: 4izh
TitleCrystal Structure of the Alpha1 dimer of Thermus thermophilus Transhydrogenase in P6
ComponentsNAD/NADP transhydrogenase alpha subunit 1
KeywordsOXIDOREDUCTASE / Alpha1 subunit / NAD binding / Domain III of Beta subunit
Function / homology
Function and homology information


proton-translocating NAD(P)+ transhydrogenase / oxidoreductase activity / nucleotide binding
Similarity search - Function
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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
proton-translocating NAD(P)(+) transhydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStout, C.D. / Yamaguchi, M. / Leung, J.
CitationJournal: To be Published
Title: Crystal structure analysis of Thermus thermophilus transhydrogenase soluble domains
Authors: Leung, J. / Yamaguchi, M. / Schurig Briccio, L.A. / B Gennis, R. / Stout, C.D.
History
DepositionJan 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: NAD/NADP transhydrogenase alpha subunit 1
B: NAD/NADP transhydrogenase alpha subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,90015
Polymers81,7032
Non-polymers1,19713
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-27 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.318, 162.318, 73.883
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
DetailsDimer of alpha1 subunit

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Components

#1: Protein NAD/NADP transhydrogenase alpha subunit 1


Mass: 40851.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Plasmid: pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) AcrAB- / References: UniProt: Q72GR8, EC: 1.6.1.2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.44 Å3/Da / Density % sol: 64.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 3.5
Details: MemStart MemSys kit, condition E2: 0.1M Sodium chloride, 0.1M Na citrate pH 3.5, 0.1M Lithium sulphate, 30% v/v PEG 400, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2012 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, Si(111); asymmetric cut 4.965 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→140.61 Å / Num. all: 98204 / Num. obs: 97773 / % possible obs: 99.52 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 25.81 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 5 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.7 / Num. unique all: 15023 / Rsym value: 0.437 / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L7D

1l7d


Resolution: 1.8→140.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.706 / SU ML: 0.071 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.018 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18024 5210 5.1 %RANDOM
Rwork0.16687 ---
all0.16754 98204 --
obs0.16754 97733 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.759 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→140.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5452 0 78 193 5723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225659
X-RAY DIFFRACTIONr_angle_refined_deg1.5252.0047662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38623.178214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1915980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.181551
X-RAY DIFFRACTIONr_chiral_restr0.1130.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214143
X-RAY DIFFRACTIONr_mcbond_it0.9411.53634
X-RAY DIFFRACTIONr_mcangle_it1.6625839
X-RAY DIFFRACTIONr_scbond_it2.71532025
X-RAY DIFFRACTIONr_scangle_it4.634.51816
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 381 -
Rwork0.254 6805 -
obs-6805 94.05 %

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