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- PDB-1nm5: R. rubrum transhydrogenase (dI.Q132N)2(dIII)1 asymmetric complex -

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Basic information

Entry
Database: PDB / ID: 1nm5
TitleR. rubrum transhydrogenase (dI.Q132N)2(dIII)1 asymmetric complex
Components(NAD(P) transhydrogenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / asymmetric complex / Rossman domain
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
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 / isomorphous replacement / Resolution: 2.4 Å
AuthorsVan Boxel, G.I. / Quirk, P.G. / Cotton, N.P. / White, S.A. / Jackson, J.B.
Citation
Journal: Biochemistry / Year: 2003
Title: Glutamine 132 in the NAD(H)-binding component of proton-translocating transhydrogenase tethers the nucleotides before hydride transfer.
Authors: van Boxel, G.I. / Quirk, P.G. / Cotton, N.P. / White, S.A. / Jackson, J.B.
#1: Journal: 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 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600THE NAD CO-FACTOR BOUND TO CHAIN B (NAD 500) IS PARTIALLY DISORDERED AND THUS SEVERAL ATOMS ARE ...THE NAD CO-FACTOR BOUND TO CHAIN B (NAD 500) IS PARTIALLY DISORDERED AND THUS SEVERAL ATOMS ARE MISSING IN THE ELECTRON DENSITY.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2697
Polymers102,1073
Non-polymers2,1624
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-43 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.939, 73.886, 205.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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NAD(P) transhydrogenase subunit ... , 2 types, 3 molecules ABC

#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: 40310.762 Da / Num. of mol.: 2 / Mutation: Q132N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: PNT / 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 NADP(H)-binding component / dIII


Mass: 21485.510 Da / Num. of mol.: 1 / Fragment: NADP-binding component
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: PNT / Production host: Escherichia coli (E. coli)
References: UniProt: Q59765, UniProt: Q2RSB4*PLUS, EC: 1.6.1.2

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Non-polymers , 4 types, 71 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop / Details: Cotton, N.P.J., (2001) Structure, 9, 165.
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: ID14-4
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 42929 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 57 Å2 / Rsym value: 0.06 / Net I/σ(I): 17.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 5828 / Rsym value: 0.551 / % possible all: 93.4
Reflection
*PLUS
Num. obs: 41317 / Num. measured all: 120855 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 93.4 % / Num. unique obs: 5828 / Num. measured obs: 15572 / Rmerge(I) obs: 0.551

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Processing

Software
NameVersionClassification
REFMAC5.1.25refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: isomorphous replacement
Starting model: PDB ENTRY 1HZZ

1hzz


Resolution: 2.4→100 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.783 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.374 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26376 1991 4.4 %RANDOM
Rwork0.23635 ---
obs0.23765 41317 90.94 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.246 Å2
Baniso -1Baniso -2Baniso -3
1-2.97 Å20 Å20 Å2
2--3.22 Å20 Å2
3----6.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6593 0 125 67 6785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226827
X-RAY DIFFRACTIONr_bond_other_d0.0020.026519
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9989268
X-RAY DIFFRACTIONr_angle_other_deg0.891315176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915887
X-RAY DIFFRACTIONr_chiral_restr0.070.21124
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027415
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021193
X-RAY DIFFRACTIONr_nbd_refined0.1860.21386
X-RAY DIFFRACTIONr_nbd_other0.2120.27460
X-RAY DIFFRACTIONr_nbtor_other0.0850.24322
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1410.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0360.21
X-RAY DIFFRACTIONr_mcbond_it0.5351.54433
X-RAY DIFFRACTIONr_mcangle_it0.97627144
X-RAY DIFFRACTIONr_scbond_it1.13632394
X-RAY DIFFRACTIONr_scangle_it1.9344.52124
LS refinement shellResolution: 2.361→2.4 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.391 146
Rwork0.358 2605
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.79270.34040.85590.58030.40541.41450.0203-0.07850.37260.19590.0922-0.0442-0.21830.3403-0.11250.64940.00880.01010.3391-0.06290.7052.746-3.27129.591
22.00980.5929-0.41391.1042-0.28611.0630.1628-0.17430.26720.3075-0.05130.2081-0.26720.1794-0.11150.3945-0.03460.05310.046-0.08250.2778-9.2570.94431.532
31.0890.6349-0.40220.3625-0.46281.23450.03270.0406-0.15740.10310.0432-0.0721-0.1645-0.2098-0.07580.26220.10910.00410.11710.02730.303-25.231-30.96233.231
41.83971.0518-0.07660.80710.01091.07790.1228-0.1269-0.28510.1035-0.0841-0.15750.08440.0311-0.03870.21870.0484-0.05450.07350.05610.349-15.198-35.68630.661
51.44150.2470.47691.51040.0692.9146-0.04440.4583-0.05020.09020.1862-0.11120.1479-0.422-0.14180.1305-0.0457-0.00930.3881-0.02820.1727-29.012-27.6062.497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2211 - 221
2X-RAY DIFFRACTION2AA238 - 360238 - 360
3X-RAY DIFFRACTION3BB1 - 2191 - 219
4X-RAY DIFFRACTION4BB242 - 371242 - 371
5X-RAY DIFFRACTION5CC30 - 20230 - 202
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.264 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.325

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