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- PDB-3v0t: Crystal Structure of Perakine Reductase, Founder Member of a Nove... -

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Basic information

Entry
Database: PDB / ID: 3v0t
TitleCrystal Structure of Perakine Reductase, Founder Member of a Novel AKR Subfamily with Unique Conformational Changes during NADPH Binding
ComponentsPerakine Reductase
KeywordsOXIDOREDUCTASE / Perakine Reductase / AKR superfamily
Function / homology
Function and homology information


perakine reductase / alkaloid metabolic process / aldo-keto reductase (NADPH) activity / cytoplasm
Similarity search - Function
NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE / Perakine reductase
Similarity search - Component
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.333 Å
AuthorsSun, L. / Chen, Y. / Rajendran, C. / Panjikar, S. / Mueller, U. / Wang, M. / Rosenthal, C. / Mindnich, R. / Penning, T.M. / Stoeckigt, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of perakine reductase, founding member of a novel aldo-keto reductase (AKR) subfamily that undergoes unique conformational changes during NADPH binding.
Authors: Sun, L. / Chen, Y. / Rajendran, C. / Mueller, U. / Panjikar, S. / Wang, M. / Mindnich, R. / Rosenthal, C. / Penning, T.M. / Stockigt, J.
History
DepositionDec 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Perakine Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8302
Polymers37,3231
Non-polymers5071
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.501, 54.501, 200.358
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Perakine Reductase


Mass: 37322.809 Da / Num. of mol.: 1 / Mutation: A213W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Gene: PR / Production host: Escherichia coli (E. coli) / References: UniProt: Q3L181
#2: Chemical ChemComp-ATR / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.3 Å3/Da / Density % sol: 46.56 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→47.199 Å / Num. obs: 15455 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ0

1pz0


Resolution: 2.333→20 Å / SU ML: 0.69 / σ(F): 2.02 / Phase error: 21.25 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2545 1553 10.05 %
Rwork0.2146 --
obs0.2186 14294 99.6 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.86 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3534 Å20 Å2-0 Å2
2--0.3534 Å20 Å2
3----0.7067 Å2
Refinement stepCycle: LAST / Resolution: 2.333→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 31 26 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082305
X-RAY DIFFRACTIONf_angle_d1.2993125
X-RAY DIFFRACTIONf_dihedral_angle_d16.166852
X-RAY DIFFRACTIONf_chiral_restr0.117355
X-RAY DIFFRACTIONf_plane_restr0.005390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3329-2.40820.31081330.2467118496
2.4082-2.49430.30251390.22511245100
2.4943-2.59420.26221350.23091246100
2.5942-2.71220.3151400.21821243100
2.7122-2.85520.27711380.22741240100
2.8552-3.0340.3161370.2141253100
3.034-3.26820.26151390.2181245100
3.2682-3.5970.23871480.19811269100
3.597-4.11730.20771450.19231280100
4.1173-5.18630.22141400.18411303100
5.1863-47.20890.26841590.25161394100
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)
10.01280.03030.02670.06240.02050.34240.0375-0.00040.11480.0304-0.05850.3413-0.0575-0.31850.00070.323-0.12510.04050.2429-0.04310.316213.34833.70669.1604
20.0053-0.0001-0.00090.0150.00190.0107-0.0459-0.0490.00420.04440.0255-0.0101-0.0287-0.0060.00020.7197-0.2520.07120.4105-0.04090.432411.1874-8.326730.6754
30.00870.01850.01860.03070.03750.053-0.02580.0251-0.050.0789-0.0520.22810.1655-0.1628-0.18560.5353-0.41060.04730.2279-0.09330.29114.0406-13.367914.8988
40.05030.0013-0.01950.0078-0.01420.0660.0289-0.0558-0.10920.084-0.0578-0.0951-0.03430.044-0.0340.4121-0.3187-0.0308-0.0385-0.03330.230631.81825.481917.2566
50.01320.0161-0.00050.0213-0.00390.01360.0215-0.0387-0.02660.1009-0.06-0.0591-0.05250.02710.00010.3963-0.1069-0.0010.20860.01950.274935.047711.328111.3235
60.0043-0.0016-00.000700.0023-0.00360.00430.04240.0021-0.0067-0.02480.00270.0321-0.00020.7022-0.2284-0.08790.54860.07860.658551.835230.381626.7695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:85)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 86:100)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 101:173)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 174:282)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 283:310)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 330:336)

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