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- PDB-3hc2: Crystal Structure of chicken sulfite oxidase mutant Tyr 322 Phe -

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Basic information

Entry
Database: PDB / ID: 3hc2
TitleCrystal Structure of chicken sulfite oxidase mutant Tyr 322 Phe
Componentssulfite oxidase
KeywordsOXIDOREDUCTASE / molybdenum / molybdopterin / sulfite oxidase / oxotransferase / metal binding
Function / homology
Function and homology information


Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MOLYBDENUM ATOM / Chem-MTE
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsQiu, J.A.
CitationJournal: To be Published
Title: Structure function studies in sulfite oxidase with altered active sites
Authors: Qiu, J.A. / Rajagopalan, K.V.
History
DepositionMay 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)51,4763
Polymers50,9851
Non-polymers4912
Water1,946108
1
A: sulfite oxidase
hetero molecules

A: sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9536
Polymers101,9702
Non-polymers9834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4540 Å2
ΔGint-47 kcal/mol
Surface area28710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.449, 86.449, 153.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

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Components

#1: Protein sulfite oxidase


Mass: 50985.188 Da / Num. of mol.: 1 / Mutation: Y322F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: sulfite oxidase / Plasmid: pTRC99a rCSO Y322F / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000
#2: 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
#3: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% PEG 5000 MME, 100 mM Magnesium acetate, 100 mM Sodium Citrate pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97903 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.5→47.84 Å / Num. all: 19498 / Num. obs: 19498 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.063 / Net I/σ(I): 39.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.331 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A99

2a99


Resolution: 2.5→47.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 12.891 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22183 996 5.1 %RANDOM
Rwork0.17522 ---
obs0.17749 18487 99.88 %-
all-19498 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.545 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å2-0 Å2-0 Å2
2--1.41 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 25 108 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222987
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9674092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0345371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00522.29131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77615432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8311531
X-RAY DIFFRACTIONr_chiral_restr0.0840.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222364
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.581.51862
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11523007
X-RAY DIFFRACTIONr_scbond_it1.84331125
X-RAY DIFFRACTIONr_scangle_it3.1024.51085
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 75 -
Rwork0.25 1347 -
obs--99.03 %
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)
11.72870.39730.05782.22270.69443.23690.00960.05880.2397-0.1947-0.02570.1469-0.9347-0.12420.01610.31310.09110.00430.13260.02590.04052.7728.078-6.629
20.83940.1958-0.50291.5280.2294.21940.00210.11270.063-0.0234-0.0160.0172-0.2724-0.10190.01390.1470.0273-0.00730.23440.01270.07794.21317.46-8.778
30.92750.437-0.6051.7689-0.25692.57690.0649-0.2232-0.01740.2312-0.0835-0.1245-0.24840.30040.01860.12430.0134-0.01040.2591-0.00250.05614.35111.5543.523
41.89890.81790.07042.99050.13932.51310.0789-0.18570.13990.566-0.01690.4425-0.1982-0.4112-0.0620.14690.05210.09590.2723-0.01870.1112-8.7988.18111.875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A95 - 173
2X-RAY DIFFRACTION2A174 - 303
3X-RAY DIFFRACTION3A304 - 382
4X-RAY DIFFRACTION4A383 - 466

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