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- PDB-1xlt: Crystal structure of Transhydrogenase [(domain I)2:domain III] he... -

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Basic information

Entry
Database: PDB / ID: 1xlt
TitleCrystal structure of Transhydrogenase [(domain I)2:domain III] heterotrimer complex
Components(NAD(P) transhydrogenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Transhydrogenase / NAD / NADH / NADP / NADPH
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 / NAD binding / NADP binding / membrane => GO:0016020 / 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
sucrose / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-NDP / 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 / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSundaresan, V. / Chartron, J. / Yamaguchi, M. / Stout, C.D.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Conformational Diversity in NAD(H) and Transhydrogenase Nicotinamide Nucleotide Binding Domains
Authors: Sundaresan, V. / Chartron, J. / Yamaguchi, M. / Stout, C.D.
History
DepositionSep 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: NAD(P) transhydrogenase subunit alpha part 1
B: NAD(P) transhydrogenase subunit alpha part 1
C: NAD(P) transhydrogenase subunit beta
D: NAD(P) transhydrogenase subunit alpha part 1
E: NAD(P) transhydrogenase subunit alpha part 1
F: NAD(P) transhydrogenase subunit beta
G: NAD(P) transhydrogenase subunit alpha part 1
H: NAD(P) transhydrogenase subunit alpha part 1
I: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,20726
Polymers298,5319
Non-polymers7,67617
Water00
1
A: NAD(P) transhydrogenase subunit alpha part 1
B: NAD(P) transhydrogenase subunit alpha part 1
C: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2909
Polymers99,5103
Non-polymers2,7806
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-51 kcal/mol
Surface area34870 Å2
MethodPISA
2
D: NAD(P) transhydrogenase subunit alpha part 1
E: NAD(P) transhydrogenase subunit alpha part 1
F: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6278
Polymers99,5103
Non-polymers2,1165
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-50 kcal/mol
Surface area34950 Å2
MethodPISA
3
G: NAD(P) transhydrogenase subunit alpha part 1
H: NAD(P) transhydrogenase subunit alpha part 1
I: NAD(P) transhydrogenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2909
Polymers99,5103
Non-polymers2,7806
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-50 kcal/mol
Surface area34310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.372, 171.082, 203.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsCrystal structure shows a dimer of domain I complexed with a monomer of domain III. Intact enzyme is a dimer.

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Components

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NAD(P) transhydrogenase subunit ... , 2 types, 9 molecules ABDEGHCFI

#1: Protein
NAD(P) transhydrogenase subunit alpha part 1 / Pyridine nucleotide transhydrogenase subunit alpha 1 / Nicotinamide nucleotide transhydrogenase ...Pyridine nucleotide transhydrogenase subunit alpha 1 / Nicotinamide nucleotide transhydrogenase subunit alpha 1 / Proton-translocating transhydrogenase component 1 / dI


Mass: 40324.785 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: pntAA, nntA1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q60164, UniProt: Q2RSB2*PLUS, EC: 1.6.1.2
#2: 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 NADPH / -binding component / dIII


Mass: 18860.613 Da / Num. of mol.: 3 / Fragment: residues 294-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: pntB, nntB / Production host: Escherichia coli (E. coli)
References: UniProt: Q59765, UniProt: Q2RSB4*PLUS, EC: 1.6.1.2

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Sugars , 1 types, 6 molecules

#3: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 11 molecules

#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3

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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: 53.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium Tartrate, PEG 3400, Sucrose, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→65 Å / Num. all: 58965 / Num. obs: 58965 / Observed criterion σ(I): 1.9 / Redundancy: 6.7 % / Rsym value: 0.117 / Net I/σ(I): 12.9
Reflection shellHighest resolution: 3.1 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.47

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→43.68 Å / Data cutoff high absF: 2843229.87 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.31 --random
Rwork0.232 ---
obs-58965 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.0232 Å2 / ksol: 0.298518 e/Å3
Displacement parametersBiso mean: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3.1→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19975 0 505 0 20480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NADP.PARAMNADP.TOP
X-RAY DIFFRACTION3NAD1.PARAMNAD1.TOP
X-RAY DIFFRACTION4SUC.PARAMSUC.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP

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