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- PDB-2a99: Crystal structure of recombinant chicken sulfite oxidase at resti... -

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Basic information

Entry
Database: PDB / ID: 2a99
TitleCrystal structure of recombinant chicken sulfite oxidase at resting state
ComponentsSulfite Oxidase
KeywordsOXIDOREDUCTASE / sulfite oxidase / Molybdopterin / Molybdenum
Function / homology
Function and homology information


sulfite oxidase / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / mitochondrial intermembrane space / heme binding / mitochondrion
Similarity search - Function
Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Oxidoreductase, molybdopterin binding site ...Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Immunoglobulin E-set / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MOLYBDENUM ATOM / Chem-MTE / Sulfite oxidase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsKarakas, E. / Wilson, H.L. / Graf, T.N. / Xiang, S. / Jaramillo-Busquets, S. / Rajagopalan, K.V. / Kisker, C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural insights into sulfite oxidase deficiency
Authors: Karakas, E. / Wilson, H.L. / Graf, T.N. / Xiang, S. / Jaramillo-Busquets, S. / Rajagopalan, K.V. / Kisker, C.
History
DepositionJul 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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.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: Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2535
Polymers40,6341
Non-polymers6194
Water4,252236
1
A: Sulfite Oxidase
hetero molecules

A: Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,50510
Polymers81,2682
Non-polymers1,2388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)86.004, 86.004, 154.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Cell settingtetragonal
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-2531-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sulfite Oxidase / / E.C.1.8.3.1


Mass: 40633.824 Da / Num. of mol.: 1
Fragment: Catalytic core domain and C terminal dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken)
Description: The gene is chemically synthesized based on the protein sequence of sulfite oxidase from Gallus gallus
Cellular location: Mitochondrial Intermembrane SpaceMitochondrion
Gene: SUOX / Organ: Liver / Organelle: Mitochondrion / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: P07850, sulfite oxidase

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Non-polymers , 5 types, 240 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#4: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.5 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, Magnesium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2003
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 28243 / Num. obs: 27999 / % possible obs: 99.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.083
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.599 / % possible all: 99.7

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Phasing

Phasing MRRfactor: 0.369 / Cor.coef. Fo:Fc: 0.632
Highest resolutionLowest resolution
Rotation3.5 Å43.01 Å
Translation3.5 Å43.01 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SOX

1sox


Resolution: 2.202→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 7.199 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1424 5.1 %RANDOM
Rwork0.149 ---
all0.15 28243 --
obs0.15 27994 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.247 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å20 Å2
2--2.19 Å20 Å2
3----4.39 Å2
Refinement stepCycle: LAST / Resolution: 2.202→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 32 236 3139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222993
X-RAY DIFFRACTIONr_bond_other_d0.0010.022707
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9694099
X-RAY DIFFRACTIONr_angle_other_deg1.24536278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1045371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.60522.29131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93215432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9071531
X-RAY DIFFRACTIONr_chiral_restr0.0920.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02621
X-RAY DIFFRACTIONr_nbd_refined0.2080.3547
X-RAY DIFFRACTIONr_nbd_other0.2330.32689
X-RAY DIFFRACTIONr_nbtor_refined0.1850.51410
X-RAY DIFFRACTIONr_nbtor_other0.0990.51640
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5337
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.518
X-RAY DIFFRACTIONr_mcbond_it1.0561.52327
X-RAY DIFFRACTIONr_mcbond_other0.1671.5744
X-RAY DIFFRACTIONr_mcangle_it1.25623007
X-RAY DIFFRACTIONr_scbond_it1.95931347
X-RAY DIFFRACTIONr_scangle_it2.9534.51092
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 108 -
Rwork0.202 1956 -
all-2064 -
obs--98.85 %
Refinement TLS params.Method: refined / Origin x: 42.2396 Å / Origin y: 16.3585 Å / Origin z: 1.1673 Å
111213212223313233
T-0.1279 Å2-0.0691 Å2-0.0166 Å2--0.042 Å20.0203 Å2---0.1191 Å2
L0.7543 °2-0.2599 °2-0.295 °2-1.409 °20.0795 °2--1.684 °2
S0.0096 Å °0.0187 Å °0.0191 Å °-0.0751 Å °-0.0351 Å °-0.1238 Å °-0.2843 Å °0.1349 Å °0.0255 Å °
Refinement TLS groupSelection: ALL

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