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- PDB-2ox6: Crystal structure of gene product SO3848 from Shewanella oneidens... -

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Basic information

Entry
Database: PDB / ID: 2ox6
TitleCrystal structure of gene product SO3848 from Shewanella oneidensis MR-1
ComponentsHypothetical protein SO3848
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Shewanella oneidensis / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


DNA binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF4447 / Domain of unknown function (DUF4447) / Putative cytoplasmic protein / YdiL domain superfamily / Putative cytoplasmic protein / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DUF4447 domain-containing protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsZhang, R. / Bigelow, L. / Giuliani, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of gene product SO3848 from Shewanella oneidensis MR-1
Authors: Zhang, R. / Bigelow, L. / Giuliani, S. / Joachimiak, A.
History
DepositionFeb 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 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_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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Hypothetical protein SO3848
B: Hypothetical protein SO3848
C: Hypothetical protein SO3848
D: Hypothetical protein SO3848
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,59714
Polymers75,3534
Non-polymers24310
Water14,034779
1
A: Hypothetical protein SO3848
B: Hypothetical protein SO3848
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7746
Polymers37,6772
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-32 kcal/mol
Surface area16840 Å2
MethodPISA
2
C: Hypothetical protein SO3848
D: Hypothetical protein SO3848
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8238
Polymers37,6772
Non-polymers1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-34 kcal/mol
Surface area16830 Å2
MethodPISA
3
C: Hypothetical protein SO3848
D: Hypothetical protein SO3848
hetero molecules

A: Hypothetical protein SO3848
B: Hypothetical protein SO3848
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,59714
Polymers75,3534
Non-polymers24310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_745-x+2,y-1/2,-z+1/21
Buried area6750 Å2
ΔGint-99 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.068, 88.680, 117.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein existed as dimer. The deposited structure (MolA/B, MolC/D) represents two dimers in the asymmetric unit.

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Components

#1: Protein
Hypothetical protein SO3848


Mass: 18838.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_3848 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8EAP9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.0M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, 1% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.7→70.71 Å / Num. all: 75810 / Num. obs: 71755 / % possible obs: 94.65 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 26.25
Reflection shellResolution: 1.7→1.746 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.2 / % possible all: 56.42

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→70.71 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.273 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.122
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 3795 5 %RANDOM
Rwork0.19901 ---
obs0.20105 71755 94.65 %-
all-71755 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.728 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--0.74 Å20 Å2
3----0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.042 Å0.04 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 1.7→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5176 0 10 779 5965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225263
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9697147
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9315644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54725.663249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83215954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5481524
X-RAY DIFFRACTIONr_chiral_restr0.0880.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023928
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22583
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23712
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2618
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.340.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.265
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4280.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.53317
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15925227
X-RAY DIFFRACTIONr_scbond_it1.98632210
X-RAY DIFFRACTIONr_scangle_it3.1254.51920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 182 -
Rwork0.284 3110 -
obs--56.42 %
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)
11.3209-0.5114-0.40090.46890.14760.9430.00860.05030.08530.044-0.0168-0.0312-0.10050.02870.0081-0.0688-0.0279-0.0058-0.01410.0022-0.117362.03831.2311.826
22.351-0.5585-0.61620.39430.09940.8576-0.0472-0.2161-0.17840.0230.02410.02770.09970.07870.0231-0.084-0.0001-0.00720.00720.0259-0.126475.76912.60314.238
31.4951-0.624-0.3060.84810.45271.07370.03270.02130.1284-0.0618-0.049-0.0378-0.0534-0.00990.0163-0.077-0.01830.0043-0.04770.0217-0.116755.225-11.83511.553
43.1086-0.4797-1.08890.3285-0.02481.1853-0.1876-0.1199-0.26120.01110.05790.04190.24440.10470.12970.01010.00250.003-0.06730.0159-0.137266.822-31.87714.391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 805 - 80
2X-RAY DIFFRACTION1AA81 - 16681 - 166
3X-RAY DIFFRACTION2BB5 - 805 - 80
4X-RAY DIFFRACTION2BB81 - 16681 - 166
5X-RAY DIFFRACTION3CC4 - 804 - 80
6X-RAY DIFFRACTION3CC81 - 16681 - 166
7X-RAY DIFFRACTION4DD6 - 806 - 80
8X-RAY DIFFRACTION4DD81 - 16681 - 166

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