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- PDB-4bk8: Superoxide reductase (Neelaredoxin) from Ignicoccus hospitalis -

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Basic information

Entry
Database: PDB / ID: 4bk8
TitleSuperoxide reductase (Neelaredoxin) from Ignicoccus hospitalis
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.847 Å
AuthorsRomao, C.V. / Matias, P.M. / Pinho, F.G. / Sousa, C.M. / Barradas, A.R. / Pinto, A.F. / Teixeira, M. / Bandeiras, T.M.
Citation
Journal: To be Published
Title: Structure of a Natural Sor Mutant
Authors: Pinho, F.G. / Romao, C.V. / Pinto, A.F. / Matias, P.M. / Teixeira, M. / Bandeiras, T.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Cloning, Purification, Crystallization and X-Ray Crystallographic Analysis of Ignicoccus Hospitalis Neelaredoxin.
Authors: Pinho, F.G. / Romao, C.V. / Pinto, A.F. / Saraiva, L.M. / Huber, H. / Matias, P.M. / Teixeira, M. / Bandeiras, T.M.
History
DepositionApr 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1692
Polymers14,1131
Non-polymers561
Water1,838102
1
A: DESULFOFERRODOXIN, FERROUS IRON-BINDING REGION
hetero molecules

A: DESULFOFERRODOXIN, FERROUS IRON-BINDING REGION
hetero molecules

A: DESULFOFERRODOXIN, FERROUS IRON-BINDING REGION
hetero molecules

A: DESULFOFERRODOXIN, FERROUS IRON-BINDING REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6768
Polymers56,4524
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area9400 Å2
ΔGint-43.7 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.995, 108.995, 61.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 14113.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) IGNICOCCUS HOSPITALIS (archaea) / 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 / Iron


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


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.76 Å3/Da / Density % sol: 67.32 %
Description: THE 3D STRUCTURE WAS SOLVED FROM A SAD DATASET MEASURED IN-HOUSE TO 2.4A AND A PRELIMINARY REFINEMENT CARRIED OUT. FOLLOWING A MOLECULAR REPLACEMENT STEP TO CORRECTLY POSITION THE ...Description: THE 3D STRUCTURE WAS SOLVED FROM A SAD DATASET MEASURED IN-HOUSE TO 2.4A AND A PRELIMINARY REFINEMENT CARRIED OUT. FOLLOWING A MOLECULAR REPLACEMENT STEP TO CORRECTLY POSITION THE RESULTING MODEL IN THE UNIT CELL OF THE CRYSTAL MEASURED AT THE ESRF, IT WAS USED IN THE FINAL REFINEMENT.
Crystal growpH: 8.5
Details: 85 MM TRISHCL PH 8.5, 8.5 MM NICL2, 15%(V/V) PEG 2000 MONOMETHYL ETHER AND 15%(V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2009 / Details: BENT CYLINDRICAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→47.2 Å / Num. obs: 18718 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.23
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.14 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PRELIMINARY MODEL FROM SAD

Resolution: 1.847→47.196 Å / SU ML: 0.14 / σ(F): 1.88 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 968 5.2 %
Rwork0.1777 --
obs0.1788 18715 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.847→47.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 0 1 102 1092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071023
X-RAY DIFFRACTIONf_angle_d1.0511394
X-RAY DIFFRACTIONf_dihedral_angle_d14.831382
X-RAY DIFFRACTIONf_chiral_restr0.08144
X-RAY DIFFRACTIONf_plane_restr0.006180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8469-1.94430.29561450.28862444X-RAY DIFFRACTION98
1.9443-2.06610.23671340.23062507X-RAY DIFFRACTION100
2.0661-2.22560.24421280.2062530X-RAY DIFFRACTION100
2.2256-2.44960.23431520.18162515X-RAY DIFFRACTION99
2.4496-2.8040.2261530.18322509X-RAY DIFFRACTION99
2.804-3.53260.18521380.16742557X-RAY DIFFRACTION99
3.5326-47.21160.1671180.15962685X-RAY DIFFRACTION96
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)
10.00360-0.02090.0090.04350.0450.0505-0.07080.508-0.53650.02790.16470.0153-0.2578-0.00010.4613-0.04550.00250.3027-0.01560.3563-50.297821.31233.8024
20.19270.07140.07630.02720.02560.10690.01350.55450.4151-0.46010.2498-0.3374-1.36230.57060.00030.6126-0.09390.04910.40680.00930.5333-46.186822.2383-8.1259
30.1349-0.1057-0.02760.05450.0449-0.0024-0.17260.39710.2316-0.37020.2558-0.3379-0.56660.6003-0.00040.4669-0.07350.0540.50310.05710.4831-42.652615.401-12.7641
40.256-0.08150.04930.06370.21250.4870.14630.8427-0.1213-0.3973-0.12730.106-0.2135-0.0805-0.00070.45840.0281-0.08080.47920.01050.2761-63.18498.4412-20.556
50.06690.04640.00290.02830.02480.04320.39920.0452-0.4091-0.12960.3064-0.39330.37250.31590.00070.37630.00390.00840.3689-0.06690.5049-38.41775.8239-9.0085
60.12790.2175-0.17580.3403-0.06820.51770.00450.29060.2569-0.0382-0.0331-0.0272-0.1602-0.1251-00.38240.0474-0.03060.28290.0030.3632-61.006712.5752-5.812
70.20390.31550.10280.46760.23580.1998-0.0417-0.07460.05650.1607-0.0848-0.1293-0.13540.105600.34670.0041-0.00910.30730.0220.3513-49.82621.5538-7.8358
80.0001-0.0903-0.05430.65420.09550.3841-0.10210.06730.0039-0.12550.082-0.0299-0.22730.05700.34730.0276-0.01780.3070.02380.2959-59.04559.3413-11.9237
90.4129-0.0031-0.44590.49410.45650.67590.0059-0.28220.4184-0.11510.007-0.0484-0.2035-0.2802-0.00040.39740.0135-0.0190.27780.05940.4095-54.129215.4585-11.2044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 7 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 8 THROUGH 16 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 17 THROUGH 30 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 31 THROUGH 46 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 47 THROUGH 57 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 58 THROUGH 74 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 75 THROUGH 89 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 90 THROUGH 109 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 110 THROUGH 124 )

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