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- PDB-1xdy: Structural and Biochemical Identification of a Novel Bacterial Ox... -

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Basic information

Entry
Database: PDB / ID: 1xdy
TitleStructural and Biochemical Identification of a Novel Bacterial Oxidoreductase, W-containing cofactor
ComponentsBacterial Sulfite Oxidase
KeywordsOXIDOREDUCTASE / Bioinformatics / sequence analysis / electron transfer / molybdoenzymes / molybdopterin
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on a heme group of donors / response to hypochlorite / oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / protein repair / molybdopterin cofactor binding / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Protein-methionine-sulfoxide reductase subunit MsrP / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-MTE / : / Protein-methionine-sulfoxide reductase catalytic subunit MsrP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLoschi, L. / Brokx, S.J. / Hills, T.L. / Zhang, G. / Bertero, M.G. / Lovering, A.L. / Weiner, J.H. / Strynadka, N.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural and biochemical identification of a novel bacterial oxidoreductase.
Authors: Loschi, L. / Brokx, S.J. / Hills, T.L. / Zhang, G. / Bertero, M.G. / Lovering, A.L. / Weiner, J.H. / Strynadka, N.C.
History
DepositionSep 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The authors believe that there is an an error in the database sequence since the other E. ...SEQUENCE The authors believe that there is an an error in the database sequence since the other E.coli strains with published sequences like the pathogenic strains O157:H7 EDL933, and CFT073 also have an Asp at that position.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterial Sulfite Oxidase
B: Bacterial Sulfite Oxidase
C: Bacterial Sulfite Oxidase
D: Bacterial Sulfite Oxidase
E: Bacterial Sulfite Oxidase
F: Bacterial Sulfite Oxidase
G: Bacterial Sulfite Oxidase
H: Bacterial Sulfite Oxidase
I: Bacterial Sulfite Oxidase
J: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,45530
Polymers336,66310
Non-polymers5,79220
Water3,999222
1
A: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Bacterial Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2453
Polymers33,6661
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.842, 177.513, 104.214
Angle α, β, γ (deg.)90.00, 109.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bacterial Sulfite Oxidase


Mass: 33666.258 Da / Num. of mol.: 10 / Fragment: residues 45-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Plasmid details: plasmid pMSYZ3 (construcy with YedYZ cloned) which is derived from plasmid pMS119
Plasmid: pMSYZ3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 and SBJ20 / References: UniProt: P76342
#2: Chemical
ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: W
#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.: 10 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 43.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG3350, Magnesium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.54 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 146127 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 37.4 Å2
Reflection shellResolution: 2.2→2.31 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XDQ

1xdq


Resolution: 2.2→38.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2806313.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 4387 3 %RANDOM
Rwork0.226 ---
obs0.226 144652 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0442 Å2 / ksol: 0.307329 e/Å3
Displacement parametersBiso mean: 56.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.42 Å20 Å2-1.51 Å2
2--4.26 Å20 Å2
3---1.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20897 0 250 222 21369
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.15
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.371.5
X-RAY DIFFRACTIONc_mcangle_it5.82
X-RAY DIFFRACTIONc_scbond_it5.782
X-RAY DIFFRACTIONc_scangle_it7.492.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 729 3.1 %
Rwork0.315 23146 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3WTE.PARWTE.TOP

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