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- PDB-1q1w: Crystal Structure of Putidaredoxin Reductase from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 1q1w
TitleCrystal Structure of Putidaredoxin Reductase from Pseudomonas putida
ComponentsPutidaredoxin reductase
KeywordsOXIDOREDUCTASE / glutathione reductase fold
Function / homology
Function and homology information


putidaredoxin-NAD+ reductase / (+)-camphor catabolic process / oxidoreductase activity, acting on NAD(P)H / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Reductase, C-terminal / Reductase C-terminal / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Reductase, C-terminal / Reductase C-terminal / : / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Putidaredoxin reductase CamA
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSevrioukova, I.F. / Li, H. / Poulos, T.L.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of putidaredoxin reductase from Pseudomonas putida, the final structural component of the cytochrome P450cam monooxygenase.
Authors: Sevrioukova, I.F. / Li, H. / Poulos, T.L.
History
DepositionJul 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_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
Remark 600HETEROGEN The het groups FAD 449 and FAD 450 are associated with chain A and chain B, respectively.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putidaredoxin reductase
B: Putidaredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1324
Polymers93,5602
Non-polymers1,5712
Water4,270237
1
A: Putidaredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5662
Polymers46,7801
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putidaredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5662
Polymers46,7801
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.040, 104.327, 166.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putidaredoxin reductase


Mass: 46780.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: CAMA / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P16640, Oxidoreductases; Acting on iron-sulfur proteins as donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: lithium sulfate, lithium acetate, lithium formate, bis-tris propane, glycerol, dithiothreitol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125-30 mg/mlprotein1drop
210 mMsodium phosphate1droppH8.0
31.5 Mlithium sulfate1reservoir
40.15 Mlithium acetate1reservoir
50.1 Mlithium formate1reservoir
62 %(v/v)glycerol1reservoir
71 mMdithiothreitol1reservoir
80.1 MTris-propane1reservoirpH8.0

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 2001 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 38331 / Num. obs: 37324 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.104 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2 / Num. unique all: 3374 / Rsym value: 0.625 / % possible all: 94.3
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 37470 / % possible obs: 97.1 %
Reflection shell
*PLUS
% possible obs: 91.3 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q1R

1q1r


Resolution: 2.6→47.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1814069.64 / Data cutoff high rms absF: 1814069.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1829 4.9 %RANDOM
Rwork0.2035 ---
all-38331 --
obs-37323 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.3881 Å2 / ksol: 0.37033 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-6.44 Å20 Å20 Å2
2---8.45 Å20 Å2
3---2.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6400 0 106 237 6743
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it2.732
X-RAY DIFFRACTIONc_scangle_it42.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.33 186 5.2 %
Rwork0.284 3374 -
obs-3374 94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.238 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28

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