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- PDB-1l7e: Crystal Structure of R. rubrum Transhydrogenase Domain I with Bou... -

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Basic information

Entry
Database: PDB / ID: 1l7e
TitleCrystal Structure of R. rubrum Transhydrogenase Domain I with Bound NADH
Componentsnicotinamide nucleotide Transhydrogenase, subunit alpha 1
KeywordsOXIDOREDUCTASE / Transhydrogenase domain I with NADH bound
Function / homology
Function and homology information


NAD(P)+ transhydrogenase (B-specific) activity / NAD(P)+ transhydrogenase (AB-specific) activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADH binding / NAD+ binding / NAD binding / protein dimerization activity
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/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 ...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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPrasad, G.S. / Wahlberg, M. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal Structures of Transhydrogenase Domain I with and without Bound NADH
Authors: Prasad, G.S. / Wahlberg, M. / Sridhar, V. / Yamaguchi, M. / Hatefi, Y. / Stout, C.D.
History
DepositionMar 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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, subunit alpha 1
B: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
C: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
D: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,6306
Polymers161,2994
Non-polymers1,3312
Water10,935607
1
A: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
B: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3153
Polymers80,6502
Non-polymers6651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-26 kcal/mol
Surface area29080 Å2
MethodPISA
2
C: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
D: nicotinamide nucleotide Transhydrogenase, subunit alpha 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3153
Polymers80,6502
Non-polymers6651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-26 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.14, 116.68, 92.60
Angle α, β, γ (deg.)90.0, 106.28, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
nicotinamide nucleotide Transhydrogenase, subunit alpha 1 / / Transhydrogenase Domain I


Mass: 40324.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q60164, UniProt: Q2RSB2*PLUS, EC: 1.6.1.1
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: mPEG 2K, Tris-HCl, Magnesium acetate, NADH, pH 7.5, VAPOR DIFFUSION, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
310 mMammonium sulfate1drop
41 mMdithiothreitol1drop
50.5 mMPMSF1drop
618 %(w/v)PEG20001reservoir
7100 mMTris-HCl1reservoirpH7.5
81 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.965 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2001
RadiationMonochromator: Curved crystal (silicon 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 326796 / Num. obs: 102189 / % possible obs: 99.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 30.9 Å2 / Rsym value: 0.119 / Net I/σ(I): 9.1
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.375 / % possible all: 99.4
Reflection
*PLUS
Num. measured all: 326796 / Rmerge(I) obs: 0.119
Reflection shell
*PLUS
Rmerge(I) obs: 0.375

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L7D

1l7d


Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.282 3047 Random
Rwork0.251 --
all0.251 102189 -
obs0.251 101562 -
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10632 0 88 607 11327
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.33
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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