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- PDB-2bbe: Crystal structure of protein SO0527 from Shewanella oneidensis -

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Basic information

Entry
Database: PDB / ID: 2bbe
TitleCrystal structure of protein SO0527 from Shewanella oneidensis
Componentshypothetical protein SO0527Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / SO0527 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


catalytic activity / monooxygenase activity / oxidoreductase activity / cytosol
Similarity search - Function
ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Antibiotic biosynthesis monooxygenase family protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsChang, C. / Bigelow, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of protein SO0527 from Shewanella oneidensis
Authors: Chang, C. / Bigelow, L. / Collart, F. / Joachimiak, A.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Sep 26, 2012Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: hypothetical protein SO0527
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5253
Polymers12,3331
Non-polymers1922
Water2,846158
1
A: hypothetical protein SO0527
hetero molecules

A: hypothetical protein SO0527
hetero molecules

A: hypothetical protein SO0527
hetero molecules

A: hypothetical protein SO0527
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,10012
Polymers49,3324
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
2
A: hypothetical protein SO0527
hetero molecules

A: hypothetical protein SO0527
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0506
Polymers24,6662
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area3660 Å2
ΔGint-56 kcal/mol
Surface area10510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.191, 94.191, 97.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-360-

HOH

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Components

#1: Protein hypothetical protein SO0527 / Hypothesis


Mass: 12332.976 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(De3) / References: UniProt: Q8EJE0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 4.37 Å3/Da / Density % sol: 71.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.0 M Ammonium sulfate 0.1 M Bis-Tris 1 % PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97956 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 23, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 15765 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 36.4
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.61 / Num. unique all: 2438 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.913 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19536 785 5 %RANDOM
Rwork0.17237 ---
all0.17347 15730 --
obs0.17347 15730 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.588 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 10 158 1002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022940
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9511289
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9885123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7624.07454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14715169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02739
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2381
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2621
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7551.5578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2042904
X-RAY DIFFRACTIONr_scbond_it2.0363414
X-RAY DIFFRACTIONr_scangle_it3.1894.5374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.971→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 49 -
Rwork0.172 1070 -
obs--97.56 %
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)
16.2102-3.2398-1.432.58351.91677.47180.01610.47310.0469-0.0357-0.08840.03280.1679-0.13910.0723-0.045-0.01070.0142-0.04730.0185-0.0197-1.55511.31-11.8
20.440.11970.28980.3359-0.14440.3551-0.0506-0.00260.04350.00470.01250.0009-0.03120.02070.0381-0.03150.0059-0.0053-0.0227-0.0244-0.00818.03711.8455.066
32.10720.01331.0280.68310.21691.5473-0.0357-0.06070.06390.146-0.00130.00370.0128-0.0410.0369-0.00630.00220.0085-0.064-0.0136-0.04475.88814.63215.408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 126 - 12
2X-RAY DIFFRACTION1AA104 - 108104 - 108
3X-RAY DIFFRACTION2AA45 - 7245 - 72
4X-RAY DIFFRACTION2AA13 - 2213 - 22
5X-RAY DIFFRACTION2AA96 - 10396 - 103
6X-RAY DIFFRACTION3AA23 - 4423 - 44
7X-RAY DIFFRACTION3AA73 - 9573 - 95

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