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- PDB-1r7s: PUTIDAREDOXIN (Fe2S2 ferredoxin), C73G mutant -

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Basic information

Entry
Database: PDB / ID: 1r7s
TitlePUTIDAREDOXIN (Fe2S2 ferredoxin), C73G mutant
ComponentsPutidaredoxin
KeywordsELECTRON TRANSFER / CYTOCHROME P450CAM / FERREDOXIN / IRON-SULFUR CLUSTER
Function / homology
Function and homology information


P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / 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 / Ubiquitin-like (UB roll) ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Putidaredoxin
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsSmith, N. / Mayhew, M. / Kelly, H. / Robinson, H. / Heroux, A. / Holden, M.J. / Gallagher, D.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of C73G putidaredoxin from Pseudomonas putida.
Authors: Smith, N. / Mayhew, M. / Holden, M.J. / Kelly, H. / Robinson, H. / Heroux, A. / Vilker, V.L. / Gallagher, D.T.
History
DepositionOct 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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_auth_seq_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.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_auth_seq_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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300BIOMOLECULE: 1, 2, 3 NUMBER OF BIOMOLECULES IN THIS ENTRY: 3 THIS ENTRY CONTAINS THE ...BIOMOLECULE: 1, 2, 3 NUMBER OF BIOMOLECULES IN THIS ENTRY: 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,6766
Polymers34,1483
Non-polymers5273
Water5,441302
1
A: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5592
Polymers11,3831
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5592
Polymers11,3831
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5592
Polymers11,3831
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.076, 78.218, 55.739
Angle α, β, γ (deg.)90.00, 111.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

DetailsThe biological unit is a monomer of 106 residues and one Fe2S2 cluster. This PDB entry (the crystal asymmetric unit) contains 3 independent copies (chains A,B,C).

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Components

#1: Protein Putidaredoxin / PDX


Mass: 11382.820 Da / Num. of mol.: 3 / Mutation: C73G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: CAMB / Production host: Escherichia coli (E. coli) / References: UniProt: P00259
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 4.31 Å3/Da / Density % sol: 71.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M Li2SO4, 0.1M Hepes, 2nM n-octanoyl sucrose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.6 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2003
RadiationMonochromator: SILICON CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 1.91→30 Å / Num. all: 45116 / Num. obs: 45116 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 6.1 / Num. unique all: 4482 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 776023.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Cluster planarity and coordination geometry were unrestrained.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2093 5 %RANDOM
Rwork0.188 ---
all0.188 44722 --
obs0.188 42076 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2734 Å2 / ksol: 0.514907 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.41 Å20 Å2-3.59 Å2
2--3.2 Å20 Å2
3---1.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.91→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 12 302 2690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d1.27
LS refinement shellResolution: 1.91→2.03 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 331 5.2 %
Rwork0.23 13085 -
obs-6135 94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FES_RELIS.PARAMFES.TOP

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