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- PDB-3qzb: Crystal structure of a putative superoxide reductase (TM0658) fro... -

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Basic information

Entry
Database: PDB / ID: 3qzb
TitleCrystal structure of a putative superoxide reductase (TM0658) from THERMOTOGA MARITIMA at 1.10 A resolution
ComponentsPutative superoxide reductase
KeywordsOXIDOREDUCTASE / IMMUNOGLOBULIN-LIKE BETA-SANDWICH / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


superoxide reductase / superoxide reductase 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
: / Putative superoxide reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative superoxide reductase (TM0658) from Thermotoga maritima at 1.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.4Feb 21, 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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Putative superoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4742
Polymers16,4191
Non-polymers561
Water3,693205
1
A: Putative superoxide reductase
hetero molecules

A: Putative superoxide reductase
hetero molecules

A: Putative superoxide reductase
hetero molecules

A: Putative superoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8988
Polymers65,6744
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area12630 Å2
ΔGint-69 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.260, 54.630, 88.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-144-

HOH

21A-242-

HOH

31A-258-

HOH

41A-328-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF TETRAMER AS BIOLOGICALLY RELEVANT STATE.

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Components

#1: Protein Putative superoxide reductase / SOR


Mass: 16418.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0658, TM_0658 / Plasmid: MH4a / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9WZC6, 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.: 205 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.

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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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 32.70% polyethylene glycol 3000, 0.1M CHES pH 9.0, Additive: 0.001 M cytidine monophosphate (CMP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97949
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 19, 2009 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.1→28.771 Å / Num. obs: 51057 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 6.511 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.15
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.1-1.140.5372.3166705012196.1
1.14-1.180.4592.9155524389196.8
1.18-1.240.3713.5199895618197.3
1.24-1.30.3234.1163794609197.8
1.3-1.390.2475.3200045588198.2
1.39-1.490.1757.3170314763198.8
1.49-1.640.11510.8185545172199.2
1.64-1.880.06617.6189515260199.7
1.88-2.370.03530.1189075255199.9
2.37-28.7710.02244.2189685391199.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→28.771 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.916 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. U VALUES : REFINED INDIVIDUALLY 3. THE STRUCTURE WAS SOLVED BASED ON ANOMALOUS DATA FROM FE. THE ENERGY WAS NOT OPTIMIZED FOR FE DURING DATA COLLECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1534 2594 5.1 %RANDOM
Rwork0.1244 ---
obs0.1259 51057 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.45 Å2 / Biso mean: 11.7974 Å2 / Biso min: 4.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.61 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.1→28.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 1 205 1264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221188
X-RAY DIFFRACTIONr_bond_other_d0.0020.02803
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9481626
X-RAY DIFFRACTIONr_angle_other_deg1.03131992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8935152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80125.47253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38715216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.402153
X-RAY DIFFRACTIONr_chiral_restr0.1220.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211346
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02223
X-RAY DIFFRACTIONr_mcbond_it2.5363724
X-RAY DIFFRACTIONr_mcbond_other1.6073285
X-RAY DIFFRACTIONr_mcangle_it3.42351206
X-RAY DIFFRACTIONr_scbond_it4.2268464
X-RAY DIFFRACTIONr_scangle_it5.79311419
X-RAY DIFFRACTIONr_rigid_bond_restr2.11231990
X-RAY DIFFRACTIONr_sphericity_free10.5293217
X-RAY DIFFRACTIONr_sphericity_bonded4.0531953
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 170 -
Rwork0.231 3466 -
all-3636 -
obs--96.06 %

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