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- PDB-3v0s: Crystal Structure of Perakine Reductase, Founder Member of a Nove... -

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Basic information

Entry
Database: PDB / ID: 3v0s
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 / oxidoreductase 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: 1.773 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_conn / 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_conn.pdbx_leaving_atom_flag / _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)37,9802
Polymers37,4731
Non-polymers5071
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.199, 55.199, 210.228
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: 37473.066 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, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#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.: 392 / 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: 2.48 Å3/Da / Density % sol: 50.35 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→48 Å / Num. obs: 37054 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ0

1pz0


Resolution: 1.773→47.804 Å / SU ML: 0.24 / σ(F): 2.02 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 1816 5 %5
Rwork0.1837 ---
obs0.1852 36288 97.62 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.359 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1552 Å20 Å2-0 Å2
2--0.1552 Å20 Å2
3----0.3104 Å2
Refinement stepCycle: LAST / Resolution: 1.773→47.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 31 392 2661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122316
X-RAY DIFFRACTIONf_angle_d1.3673143
X-RAY DIFFRACTIONf_dihedral_angle_d13.421863
X-RAY DIFFRACTIONf_chiral_restr0.071354
X-RAY DIFFRACTIONf_plane_restr0.008390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7734-1.82140.3421100.293208980
1.8214-1.8750.27251380.2465261998
1.875-1.93550.27341370.2161260598
1.9355-2.00470.23921390.1957263499
2.0047-2.08490.21461410.1737266699
2.0849-2.17980.20921410.1716268199
2.1798-2.29470.23311400.1753265699
2.2947-2.43850.20881400.1689265799
2.4385-2.62680.20921430.1635271399
2.6268-2.89110.21041430.163270699
2.8911-3.30940.1811420.17252725100
3.3094-4.16910.18791480.172792100
4.1691-47.82110.21391540.2028292999
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)
10.05030.0248-0.04050.0271-0.03760.0507-0.0590.0197-0.0584-0.00760.0132-0.0320.0713-0.0149-0.00290.08330.01340.00760.12880.00570.084411.36297.905724.4407
2-0.00010.0002-0.00020.00010.00030.00010.02070.0022-0.0194-0.05260.01420.02830.0137-0.00430.00010.1670.02280.00610.2878-0.00770.1076-1.000613.97393.7036
30.0177-0.0113-0.0010.0136-0.01350.03370.02160.05520.0459-0.03170.01440.08220.0219-0.14180.0178-0.0460.0204-0.01780.22670.06670.1346-3.365217.344819.9352
40.0087-0.00610.0040.0207-0.00750.0247-0.03240.11050.0658-0.00580.018-0.0088-0.03110.093-0.0053-0.0170.0093-0.01960.24150.05360.125521.751225.359716.1667
50.0095-0.0038-0.01720.00170.00760.0345-0.01950.00020.01050.0023-0.0286-0.00340.01090.0157-0.02240.02750.0212-0.00090.16890.00280.12422.010520.569522.5013
60.02010.0092-0.00580.0054-00.0101-0.06180.0330.0358-0.0033-0.0297-0.0354-0.01910.0482-0.00050.0625-0.0008-0.02330.12010.0160.139228.446823.417123.6247
70.0126-0.0002-0.00280.0019-0.0010.0014-0.0060.0037-0.0004-0.00270.002-0.0215-0.02040.011700.16830.0332-0.0040.29930.12090.25253.663729.80159.2851
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 174:258)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 259:282)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 283:310)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 328:336)

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