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- PDB-2o3l: Crystal structure of a duf1048 protein with a left-handed superhe... -

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Basic information

Entry
Database: PDB / ID: 2o3l
TitleCrystal structure of a duf1048 protein with a left-handed superhelix fold (bce_3448) from bacillus cereus atcc 10987 at 2.05 A resolution
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyUncharacterised conserved protein UCP029876 / Protein of unknown function (DUF1048) / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_979748.1) from Bacillus cereus ATCC 10987 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: 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 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE RESULTS OF SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUE 14 OF THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1676
Polymers19,7952
Non-polymers3724
Water1,910106
1
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9892
Polymers9,8971
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1784
Polymers9,8971
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.202, 61.202, 101.702
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsTHE RESULTS OF SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Hypothetical protein /


Mass: 9897.275 Da / Num. of mol.: 2 / Fragment: residues 14-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: NP_979748.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q734F7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 0.8M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97921, 0.97942, 0.94645
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979421
30.946451
ReflectionResolution: 1.999→29.298 Å / Num. obs: 14352 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 31.23 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.05-2.15.10.6351.1530810400.63599.3
2.1-2.165.20.4931.4521710060.49399.6
2.16-2.225.20.391.851199890.3999.6
2.22-2.295.20.3012.349119440.30199.8
2.29-2.375.20.239349659490.23999.9
2.37-2.455.30.193.747879070.19100
2.45-2.545.30.1564.545638600.156100
2.54-2.655.40.1265.645238420.126100
2.65-2.765.40.1126.344178200.112100
2.76-2.95.40.097.841857740.09100
2.9-3.065.40.0759.239967430.075100
3.06-3.245.40.0561237676980.056100
3.24-3.475.30.05312.235396620.053100
3.47-3.745.30.05111.532846160.051100
3.74-4.15.20.04512.830685890.045100
4.1-4.585.30.03715.827595230.037100
4.58-5.295.10.04212.323914660.042100
5.29-6.4850.04512.820034030.045100
6.48-9.174.80.047.215763310.04100
9.17-29.34.20.0419.57921900.04196.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→29.298 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.2 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.154
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.70 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO SULFATE MOLECULES FROM CRYSTALLIZATION SOLUTION ARE INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 723 5 %RANDOM
Rwork0.184 ---
obs0.186 14319 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.43 Å20 Å2
2--0.87 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1263 0 23 106 1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221359
X-RAY DIFFRACTIONr_bond_other_d0.0010.021199
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.951841
X-RAY DIFFRACTIONr_angle_other_deg0.85832776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6995178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52425.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63615222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.518154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02281
X-RAY DIFFRACTIONr_nbd_refined0.2220.2350
X-RAY DIFFRACTIONr_nbd_other0.1690.21214
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2687
X-RAY DIFFRACTIONr_nbtor_other0.0870.2771
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.27
X-RAY DIFFRACTIONr_mcbond_it2.4873858
X-RAY DIFFRACTIONr_mcbond_other0.6583350
X-RAY DIFFRACTIONr_mcangle_it3.48951320
X-RAY DIFFRACTIONr_scbond_it6.9558579
X-RAY DIFFRACTIONr_scangle_it8.36311514
LS refinement shellResolution: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 52 -
Rwork0.253 987 -
obs-1039 99.52 %
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)
14.39172.6141.46757.04690.37112.5965-0.0129-0.2521-0.02510.3783-0.0042-0.078-0.14190.00810.0171-0.1977-0.02170.0194-0.1860.0451-0.2175-8.925127.13195.2546
20.37980.5539-1.54291.3496-1.32477.84960.0127-0.03550.02920.1032-0.04930.0419-0.37340.0310.0366-0.18380.0240.0039-0.1666-0.005-0.132-22.983917.280916.717
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA13 - 951 - 83
22BB14 - 942 - 82

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