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- PDB-1y07: Crystal structure of the superoxide reductase from Treponema pallidum -

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Basic information

Entry
Database: PDB / ID: 1y07
TitleCrystal structure of the superoxide reductase from Treponema pallidum
Componentsdesulfoferrodoxin (rbo)
KeywordsOXIDOREDUCTASE / beta-sheet / iron binding
Function / homology
Function and homology information


oxidoreductase activity / iron ion binding
Similarity search - Function
SH3 type barrels. - #10 / SH3 type barrels. / SOR catalytic domain / Desulfoferrodoxin, ferrous iron-binding domain / Desulfoferrodoxin, ferrous iron-binding domain superfamily / Desulfoferrodoxin / Other non-globular / Special / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Desulfoferrodoxin (Rbo)
Similarity search - Component
Biological speciesTreponema pallidum subsp. pallidum str. Nichols (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsSantos-Silva, T. / Trincao, J. / Carvalho, A.L. / Bonifacio, C. / Auchere, F. / Moura, J. / Romao, M.J.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2006
Title: The first crystal structure of class III superoxide reductase from Treponema pallidum.
Authors: Santos-Silva, T. / Trincao, J. / Carvalho, A.L. / Bonifacio, C. / Auchere, F. / Raleiras, P. / Moura, I. / Moura, J. / Romao, M.J.
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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 (rbo)
B: desulfoferrodoxin (rbo)
C: desulfoferrodoxin (rbo)
D: desulfoferrodoxin (rbo)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,60711
Polymers55,2804
Non-polymers3287
Water6,413356
1
A: desulfoferrodoxin (rbo)
B: desulfoferrodoxin (rbo)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8326
Polymers27,6402
Non-polymers1924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-13 kcal/mol
Surface area11620 Å2
MethodPISA
2
C: desulfoferrodoxin (rbo)
D: desulfoferrodoxin (rbo)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7765
Polymers27,6402
Non-polymers1363
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-25 kcal/mol
Surface area11700 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-58 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.311, 59.946, 65.520
Angle α, β, γ (deg.)90.00, 104.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
desulfoferrodoxin (rbo) / Superoxide Reductase


Mass: 13819.876 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum subsp. pallidum str. Nichols (bacteria)
Species: Treponema pallidum / Strain: subsp. pallidum str. Nichols / Gene: TP0823 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O83795, superoxide reductase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.2 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, magnesium chloride, trisHCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.739, 1.033
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 8, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7391
21.0331
ReflectionResolution: 1.55→63.25 Å / Num. all: 53624 / Num. obs: 53059 / % possible obs: 82.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.043 / Net I/σ(I): 8.8
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3751 / Rsym value: 0.177 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→63.25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.065 / SU ML: 0.072 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.167 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23522 2678 5 %RANDOM
Rwork0.18183 ---
all0.189 53277 --
obs0.1845 50599 82.13 %-
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: 14.824 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20.26 Å2
2--1.66 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 7 356 4087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213815
X-RAY DIFFRACTIONr_bond_other_d0.0030.023470
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9465170
X-RAY DIFFRACTIONr_angle_other_deg0.88638093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3285481
X-RAY DIFFRACTIONr_chiral_restr0.1070.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024215
X-RAY DIFFRACTIONr_gen_planes_other0.020.02741
X-RAY DIFFRACTIONr_nbd_refined0.20.2708
X-RAY DIFFRACTIONr_nbd_other0.2610.23914
X-RAY DIFFRACTIONr_nbtor_other0.0880.22410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2267
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.218
X-RAY DIFFRACTIONr_mcbond_it1.5451.52422
X-RAY DIFFRACTIONr_mcangle_it2.26823884
X-RAY DIFFRACTIONr_scbond_it3.12231393
X-RAY DIFFRACTIONr_scangle_it4.7474.51286
X-RAY DIFFRACTIONr_rigid_bond_restr1.8123815
X-RAY DIFFRACTIONr_sphericity_free6.1122363
X-RAY DIFFRACTIONr_sphericity_bonded2.4723724
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 79 -
Rwork0.191 1651 -
obs-3751 82.4 %
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)
12.7316-1.46970.29332.0143-1.11720.8744-0.0885-0.28230.09180.19280.17110.0609-0.17460.0124-0.08260.15190.00120.02850.0879-0.04830.095711.891828.226434.6249
20.9684-0.0065-0.4370.4393-0.06552.1757-0.0542-0.0958-0.01770.0683-0.0696-0.00240.02390.02590.12370.1015-0.0101-0.00050.08-0.03670.06717.994215.295829.0488
31.56580.3660.85862.36830.54942.9042-0.0420.36790.09230.06450.05080.1998-0.1471-0.0515-0.00880.09820.0310.07260.13130.03970.1903-2.339629.219424.7989
41.9282-0.5154-0.17911.9822-1.03932.3798-0.00860.4889-0.0447-0.05250.10790.2419-0.0456-0.5629-0.09930.01910.0063-0.03060.2579-0.0340.05112.106520.53612.927
51.90530.8414-0.16550.8004-0.14410.3043-0.01530.29320.0119-0.03410.04410.04710.1234-0.0702-0.02880.11420.0158-0.01630.09570.02380.088841.089526.2528-3.6729
62.15170.5089-0.26860.58140.28921.5964-0.07490.1003-0.2505-0.06440.014-0.01510.02970.01710.06090.0854-0.01010.00870.0447-0.00470.09533.672214.253.5868
71.79730.5602-0.07390.8189-0.84831.97190.0215-0.13710.18630.101-0.05480.0616-0.12120.04710.03320.10030.0046-0.00630.0607-0.00410.115352.509729.85774.9815
84.24630.9846-0.24981.1159-0.36510.36240.1987-0.86260.01340.094-0.2338-0.1017-0.03130.20410.03510.0481-0.0554-0.01850.20850.01740.022649.253922.140418.7077
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 493 - 49
2X-RAY DIFFRACTION2AA50 - 12850 - 128
3X-RAY DIFFRACTION3BB3 - 493 - 49
4X-RAY DIFFRACTION4BB50 - 12850 - 128
5X-RAY DIFFRACTION5CC3 - 493 - 49
6X-RAY DIFFRACTION6CC50 - 12850 - 128
7X-RAY DIFFRACTION7DD3 - 493 - 49
8X-RAY DIFFRACTION8DD50 - 12850 - 128

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