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- PDB-3lb8: Crystal structure of the covalent putidaredoxin reductase-putidar... -

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Basic information

Entry
Database: PDB / ID: 3lb8
TitleCrystal structure of the covalent putidaredoxin reductase-putidaredoxin complex
Components
  • Putidaredoxin
  • Putidaredoxin reductase
KeywordsOxidoreductase/Electron Transport / covalently linked protein-protein complex / FAD / Flavoprotein / Oxidoreductase / Electron transport / Iron-sulfur / Metal-binding / Oxidoreductase-Electron Transport complex
Function / homology
Function and homology information


putidaredoxin-NAD+ reductase / P450-containing electron transport chain / (+)-camphor catabolic process / oxidoreductase activity, acting on NAD(P)H / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Reductase, C-terminal / Reductase C-terminal / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / : / Adrenodoxin / FAD/NAD-linked reductase, C-terminal dimerisation domain / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / FAD/NAD-linked reductase, dimerisation domain superfamily ...Reductase, C-terminal / Reductase C-terminal / Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / : / Adrenodoxin / FAD/NAD-linked reductase, C-terminal dimerisation domain / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Ubiquitin-like (UB roll) / FAD/NAD(P)-binding domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Putidaredoxin / Putidaredoxin reductase CamA
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSevrioukova, I.F.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of the putidaredoxin reductase x putidaredoxin electron transfer complex.
Authors: Sevrioukova, I.F. / Poulos, T.L. / Churbanova, I.Y.
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,2488
Polymers117,3254
Non-polymers1,9234
Water1,11762
1
A: Putidaredoxin reductase
C: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6244
Polymers58,6622
Non-polymers9612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putidaredoxin reductase
D: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6244
Polymers58,6622
Non-polymers9612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.600, 103.400, 167.700
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: 47265.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camA / Plasmid: pET-Pdr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P16640, Oxidoreductases; Acting on iron-sulfur proteins as donors; With NAD+ or NADP+ as acceptor
#2: Protein Putidaredoxin / PDX


Mass: 11396.780 Da / Num. of mol.: 2 / Mutation: C73S, C85S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camA, camB / Plasmid: pET-Pdr / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00259
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 1.3 M malonate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Oct 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→49.5 Å / Num. all: 37043 / Num. obs: 36524 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.049 / Net I/σ(I): 25.3
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 5.6 / Rsym value: 0.144 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q1R

1q1r


Resolution: 2.6→49.5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1791504.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1846 5.1 %RANDOM
Rwork0.244 ---
obs0.244 36524 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.4633 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 75.8 Å2
Baniso -1Baniso -2Baniso -3
1--18.75 Å20 Å20 Å2
2--48.37 Å20 Å2
3----29.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7887 0 114 62 8063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
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_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 302 5 %
Rwork0.357 5728 -
obs--99.9 %

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