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- PDB-4brv: Superoxide reductase (Neelaredoxin) from Ignicoccus hospitalis E23A -

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Basic information

Entry
Database: PDB / ID: 4brv
TitleSuperoxide reductase (Neelaredoxin) from Ignicoccus hospitalis E23A
ComponentsDESULFOFERRODOXIN, FERROUS IRON-BINDING REGION
KeywordsOXIDOREDUCTASE / NEELAREDOXIN / SYMBIOSIS / OXIDATIVE STRESS
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
: / Desulfoferrodoxin, ferrous iron-binding region
Similarity search - Component
Biological speciesIGNICOCCUS HOSPITALIS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRomao, C.V. / Matias, P.M. / Pinho, F.G. / Sousa, C.M. / Barradas, A.R. / Pinto, A.F. / Teixeira, M. / Bandeiras, T.M.
CitationJournal: To be Published
Title: Structure of a Natural Sor Mutant
Authors: Romao, C.V. / Matias, P.M. / Pinho, F.G. / Sousa, C.M. / Barradas, A.R. / Pinto, A.F. / Teixeira, M. / Bandeiras, T.M.
History
DepositionJun 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Dec 20, 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 / 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_asym_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_asym_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: DESULFOFERRODOXIN, FERROUS IRON-BINDING REGION
B: DESULFOFERRODOXIN, FERROUS IRON-BINDING REGION
C: DESULFOFERRODOXIN, FERROUS IRON-BINDING REGION
D: DESULFOFERRODOXIN, FERROUS IRON-BINDING REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4448
Polymers56,2204
Non-polymers2234
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-114.5 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.908, 74.796, 68.754
Angle α, β, γ (deg.)90.00, 106.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DESULFOFERRODOXIN, FERROUS IRON-BINDING REGION / SUPEROXIDE REDUCTASE


Mass: 14055.056 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) IGNICOCCUS HOSPITALIS (archaea) / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: A8AC72
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.4 Å3/Da / Density % sol: 49.1 % / Description: NONE
Crystal growpH: 8.5
Details: 100MM TRISHCL PH 8.5, 10MM NICL2, 20% (W/V) PEG 2000 MONOMETHYLETHER AND 15% (W/V) GLYCEROL.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER PROTEUM PT135 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→40.7 Å / Num. obs: 33545 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.26 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BK8

4bk8


Resolution: 2.05→29.601 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 1561 5.1 %
Rwork0.1587 --
obs0.1608 30894 92.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→29.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 4 139 4115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074103
X-RAY DIFFRACTIONf_angle_d1.1325567
X-RAY DIFFRACTIONf_dihedral_angle_d15.0231541
X-RAY DIFFRACTIONf_chiral_restr0.084583
X-RAY DIFFRACTIONf_plane_restr0.005723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11620.32861260.27452362X-RAY DIFFRACTION81
2.1162-2.19180.28771270.24622429X-RAY DIFFRACTION85
2.1918-2.27950.28431410.22212473X-RAY DIFFRACTION86
2.2795-2.38320.24941200.19162603X-RAY DIFFRACTION89
2.3832-2.50880.20661160.1872677X-RAY DIFFRACTION92
2.5088-2.66590.25291520.192709X-RAY DIFFRACTION94
2.6659-2.87160.22021540.16812761X-RAY DIFFRACTION96
2.8716-3.16020.19271720.15972736X-RAY DIFFRACTION96
3.1602-3.61680.20771410.13662817X-RAY DIFFRACTION96
3.6168-4.55410.15261520.12082845X-RAY DIFFRACTION98
4.5541-29.60420.15191600.13032921X-RAY DIFFRACTION99
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)
11.3416-2.9961.69059.2186-1.18237.063-0.332-1.19110.44831.38940.07240.2567-0.1971-0.27890.19970.3305-0.0033-0.00620.4034-0.05310.242215.1704-16.978611.1787
26.01413.5472-0.53946.2599-0.63171.3340.1516-0.25850.54280.358-0.09630.5811-0.1251-0.0362-0.09830.17580.04030.0160.2085-0.00530.29920.0574-15.14181.9653
33.36930.90360.04313.88070.03751.3611-0.0430.03840.0995-0.09440.03880.3280.0108-0.0582-0.00620.10350.0286-0.01090.1437-0.00550.21864.8903-20.7932-0.8849
43.352-5.356-2.31919.2051.6588.0705-0.4344-1.2396-0.42730.88020.3601-0.0854-0.10470.19970.09640.3039-0.00890.04840.40950.06280.291912.3952-27.423311.1888
54.98982.1010.49238.17480.64291.38850.0403-0.1832-0.48310.50740.0088-0.44820.0470.0255-0.06440.1710.0478-0.03190.2020.00470.248727.4885-29.40032.0103
62.87090.81910.24514.6230.43331.3735-0.0240.01030.0304-0.1020.0253-0.1906-0.04540.0733-0.00730.10620.0342-0.01370.15110.00550.180422.546-23.6117-0.8791
72.77414.358-0.70286.8643-0.70637.5842-0.32991.50470.3431-1.5227-0.1105-0.63250.02970.60450.4081.07040.18450.14861.21710.22460.403715.2075-16.9191-32.3624
83.32081.076-0.42575.66830.71763.754-0.08750.99550.2577-0.90.2523-0.4245-0.12390.0274-0.1580.52880.02380.24350.69050.01460.376729.1219-24.3127-24.092
93.0097-0.31850.22522.6280.51713.08030.02720.86760.0436-0.7603-0.0313-0.18530.05670.0477-0.00270.4333-0.00460.09090.4543-0.00120.203422.4607-24.3787-20.193
103.22512.6822-3.39246.67191.93248.65710.27261.2053-0.0025-1.1089-0.25570.4223-0.333-0.10270.01670.98950.12-0.07911.1513-0.13420.341512.3523-27.2745-32.4924
114.05911.2950.81666.1929-1.96863.65510.14641.0547-0.1396-1.3278-0.32430.128-0.0116-0.19710.01610.6050.1066-0.23760.668-0.01270.3328-1.7731-19.7804-24.1403
122.9499-0.5078-0.24942.8257-0.1743.04440.00350.91720.0447-0.7904-0.07940.1392-0.0915-0.04280.01550.44270.0103-0.12610.48820.0250.24344.9951-19.9163-20.2082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:12)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 13:52)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 53:124)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:12)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 13:52)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 53:124)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 1:12)
8X-RAY DIFFRACTION8(CHAIN C AND RESID 13:47)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 48:124)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 1:12)
11X-RAY DIFFRACTION11(CHAIN D AND RESID 13:47)
12X-RAY DIFFRACTION12(CHAIN D AND RESID 48:124)

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