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- PDB-2v3b: Crystal structure of the electron transfer complex rubredoxin - r... -

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Basic information

Entry
Database: PDB / ID: 2v3b
TitleCrystal structure of the electron transfer complex rubredoxin - rubredoxin reductase from Pseudomonas aeruginosa.
Components
  • RUBREDOXIN 2
  • RUBREDOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / ALKANE DEGRADATION / IRON-SULFUR PROTEIN / ELECTRON TRANSFER / ELECTRON TRANSPORT / FAD / NAD / IRON / FLAVOPROTEIN / METAL-BINDING
Function / homology
Function and homology information


rubredoxin-NADP+ reductase activity / rubredoxin-NAD+ reductase / rubredoxin-NAD+ reductase activity / alkane catabolic process / flavin adenine dinucleotide binding / electron transfer activity / iron ion binding / cytoplasm
Similarity search - Function
Enolase-like; domain 1 - #120 / Rubredoxin binding domain / Rubredoxin binding C-terminal domain / : / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain ...Enolase-like; domain 1 - #120 / Rubredoxin binding domain / Rubredoxin binding C-terminal domain / : / Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / Single Sheet / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / Rubredoxin-2 / Rubredoxin-NAD(+) reductase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RUBREDOXIN REDUCTASE
B: RUBREDOXIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6794
Polymers46,8382
Non-polymers8412
Water4,594255
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-3.2 kcal/mol
Surface area22990 Å2
MethodPQS
Unit cell
Length a, b, c (Å)61.070, 97.150, 81.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-2104-

HOH

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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: Protein RUBREDOXIN 2 / RUBREDOXIN


Mass: 6178.095 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: Q9HTK8
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.11 Å3/Da / Density % sol: 52.17 % / Description: NONE
Crystal growDetails: 0.2M KF, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.741
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.741 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19054 / % possible obs: 90.6 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3 / % possible all: 86.2

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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 2V3A AND 1BQ8

2v3a

1bq8


Resolution: 2.45→97.13 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 14.682 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.151 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 891 5.3 %RANDOM
Rwork0.181 ---
obs0.185 15866 91.1 %-
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: 29.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.21 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.45→97.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 54 255 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223649
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.18324999
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31123.077156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6215597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6281538
X-RAY DIFFRACTIONr_chiral_restr0.0750.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022855
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.21626
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22434
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3591.52384
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.61323708
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.85631499
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4074.51288
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: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 68 -
Rwork0.24 1115 -
obs--89.35 %
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)
11.5868-0.47570.2090.31880.05850.5948-0.0096-0.0845-0.08570.0085-0.01340.03890.0787-0.06660.0229-0.0675-0.01550.0148-0.11470.0071-0.0995-6.8658-20.3676-7.0462
24.3771-0.1556-1.97012.5772-1.647910.9575-0.0324-0.5227-0.24890.326-0.11970.13570.7676-0.26460.15220.2124-0.05730.00530.07870.00530.1281-13.8999-30.869513.6641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 384
2X-RAY DIFFRACTION2B1 - 53

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