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- PDB-4d7p: Superoxide reductase (1Fe-SOR) from Giardia intestinalis -

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Basic information

Entry
Database: PDB / ID: 4d7p
TitleSuperoxide reductase (1Fe-SOR) from Giardia intestinalis
ComponentsSUPEROXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / SUPEROXIDE REDUCTASE / PATHOGEN / PROTOZOAN / PARASITE / OXIDATIVE STRESS / EUKARYOTA
Function / homology
Function and homology information


oxidoreductase activity / iron ion binding
Similarity search - Function
SOR catalytic domain / Desulfoferrodoxin, ferrous iron-binding domain / Desulfoferrodoxin, ferrous iron-binding domain superfamily / Desulfoferrodoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Desulfoferrodox domain-containing protein / Desulfoferredoxin
Similarity search - Component
Biological speciesGIARDIA INTESTINALIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsSousa, C.M. / Carpentier, P. / Matias, P.M. / Testa, F. / Pinho, F.G. / Sarti, P. / Giuffre, A. / Bandeiras, T.M. / Romao, C.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Superoxide Reductase from Giardia Intestinalis: Structural Characterization of the First Sor from a Eukaryotic Organism Shows an Iron Centre that is Highly Sensitive to Photoreduction.
Authors: Sousa, C.M. / Carpentier, P. / Matias, P.M. / Testa, F. / Pinho, F. / Sarti, P. / Giuffre, A. / Bandeiras, T.M. / Romao, C.V.
History
DepositionNov 26, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references / Structure summary
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3May 1, 2024Group: 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUPEROXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6042
Polymers12,5491
Non-polymers561
Water64936
1
A: SUPEROXIDE REDUCTASE
hetero molecules

A: SUPEROXIDE REDUCTASE
hetero molecules

A: SUPEROXIDE REDUCTASE
hetero molecules

A: SUPEROXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4178
Polymers50,1944
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_576x,-y+2,-z+11
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation2_575-x,-y+2,z1
Buried area7020 Å2
ΔGint-28.6 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.270, 90.270, 90.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-2016-

HOH

21A-2023-

HOH

31A-2026-

HOH

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Components

#1: Protein SUPEROXIDE REDUCTASE


Mass: 12548.513 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GIARDIA INTESTINALIS (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD
References: UniProt: E1EW53, UniProt: V6TJK7*PLUS, superoxide reductase
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.5 Å3/Da / Density % sol: 50 %
Description: THE SEARCH MODEL USED WAS A PRELIMINARY AND REFINED SAD DATASET MEASURED IN-HOUSE TO 2.0A.
Crystal growpH: 7 / Details: 24% DIOXANE, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98008
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 2→31.92 Å / Num. obs: 8422 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 31.44 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PRELIMINARY MODEL FROM SAD

Resolution: 2.001→31.915 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 405 4.8 %
Rwork0.1946 --
obs0.1963 8417 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.001→31.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 1 36 792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012778
X-RAY DIFFRACTIONf_angle_d1.121055
X-RAY DIFFRACTIONf_dihedral_angle_d15.973284
X-RAY DIFFRACTIONf_chiral_restr0.044113
X-RAY DIFFRACTIONf_plane_restr0.006133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0006-2.290.31841390.23272634X-RAY DIFFRACTION100
2.29-2.88490.25751430.22672640X-RAY DIFFRACTION100
2.8849-31.91930.19881230.17522738X-RAY DIFFRACTION100
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)
11.34250.0819-0.44630.1411-0.27420.62640.02880.05720.32540.23310.0806-0.23690.0652-0.09350.320.4369-0.0424-0.25160.2165-0.14850.49665.7303106.610557.3725
20.14750.07010.01110.382-0.45540.6765-0.0518-0.22570.38740.7432-0.0648-0.649-0.2340.0930.15720.233-0.0528-0.13890.2027-0.01440.52645.6449101.394652.2741
30.0591-0.0422-0.04640.12350.07070.0512-0.0187-0.08540.03830.0312-0.07120.09180.0311-0.1182-0.06660.6126-0.02130.39260.377-0.090.5856-17.089397.159661.6666
40.4882-0.03770.15320.0224-0.02530.0709-0.16270.14990.12850.3664-0.1498-0.0776-0.01530.0801-0.05040.1886-0.0056-0.010.15870.01550.29671.685298.471447.768
50.0043-0.00070.0324-0.00140.00230.276-0.0678-0.10420.00390.22280.07150.2058-0.1074-0.10510.08810.21980.06840.10120.3429-0.28960.5813-15.498103.570954.563
60.31720.1631-0.18690.2647-0.08480.21980.1537-0.3261-0.09780.7226-0.2152-0.1691-0.08060.0363-0.01150.4696-0.0428-0.08440.2283-0.03870.33492.057999.278459.5821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 16 THROUGH 26 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 27 THROUGH 56 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 57 THROUGH 62 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 63 THROUGH 83 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 84 THROUGH 91 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 92 THROUGH 111 )

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