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- PDB-2v3a: Crystal structure of rubredoxin reductase from Pseudomonas aeruginosa. -

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Basic information

Entry
Database: PDB / ID: 2v3a
TitleCrystal structure of rubredoxin reductase from Pseudomonas aeruginosa.
ComponentsRUBREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / ALKANE DEGRADATION / NADH OXIDOREDUCTASE / RUBREDOXIN REDUCTASE / FAD / NAD / FLAVOPROTEIN
Function / homology
Function and homology information


rubredoxin-NADP+ reductase activity / rubredoxin-NAD+ reductase / rubredoxin-NAD+ reductase activity / alkane catabolic process / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Enolase-like; domain 1 - #120 / Rubredoxin binding domain / Rubredoxin binding C-terminal domain / : / 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 ...Enolase-like; domain 1 - #120 / Rubredoxin binding domain / Rubredoxin binding C-terminal domain / : / 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 / DI(HYDROXYETHYL)ETHER / Rubredoxin-NAD(+) reductase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHagelueken, G. / Wiehlmann, L. / Adams, T.M. / Kolmar, H. / Heinz, D.W. / Tuemmler, B. / Schubert, W.-D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Crystal Structure of the Electron Transfer Complex Rubredoxin - Rubredoxin Reductase from Pseudomonas Aeruginosa.
Authors: Hagelueken, G. / Wiehlmann, L. / Adams, T.M. / Kolmar, H. / Heinz, D.W. / Tuemmler, B. / Schubert, W.-D.
History
DepositionJun 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RUBREDOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,15310
Polymers40,6601
Non-polymers1,4939
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)119.602, 119.602, 158.064
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein RUBREDOXIN REDUCTASE


Mass: 40659.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HTK9
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growDetails: 5% PEG 1000, 40% PEG 300, TRIS-CL PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.981
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25303 / % possible obs: 98.1 % / Observed criterion σ(I): 2.7 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / % possible all: 82.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XHC

1xhc


Resolution: 2.4→103.7 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.244 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1333 5 %RANDOM
Rwork0.166 ---
obs0.168 25303 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.23 Å20 Å2
2---0.47 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→103.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 97 231 3152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4932.0144295
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92822.824131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98715511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1531534
X-RAY DIFFRACTIONr_chiral_restr0.0940.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022397
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21371
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22059
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7081.52026
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07923154
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88731305
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8964.51126
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 80 -
Rwork0.183 1803 -
obs--98.38 %
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)
11.5729-0.17560.46372.01790.39062.1589-0.0355-0.1072-0.19680.12130.0310.04340.254-0.03230.0045-0.1395-0.01690.0717-0.10780.0443-0.091183.284729.605424.8718
21.3739-0.97860.56311.61980.05172.49470.0121-0.0078-0.2829-0.1683-0.01990.18330.2321-0.08610.0078-0.0764-0.0141-0.0004-0.1107-0.0597-0.076679.139528.1421-2.5754
31.9388-0.6316-0.25352.00510.30711.85-0.0167-0.11910.12350.00580.0464-0.2264-0.08940.1955-0.0297-0.1644-0.0170.0204-0.1206-0.0066-0.129291.395242.205322.913
43.67741.3784-0.31591.6911-0.27942.7640.03650.18770.1856-0.3464-0.0064-0.1365-0.270.2462-0.0301-0.07710.01710.0777-0.01410.006-0.0217104.09137.72580.9397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 130
2X-RAY DIFFRACTION2A131 - 240
3X-RAY DIFFRACTION3A241 - 310
4X-RAY DIFFRACTION4A311 - 384

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