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- PDB-2o35: Protein of Unknown Function (DUF1244) from Sinorhizobium meliloti -

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Basic information

Entry
Database: PDB / ID: 2o35
TitleProtein of Unknown Function (DUF1244) from Sinorhizobium meliloti
ComponentsHypothetical protein DUF1244Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / helix bundle / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySMc04008-like fold / SMc04008-like / SMc04008-like domain / SMc04008-like superfamily / Protein of unknown function (DUF1244) / Orthogonal Bundle / Mainly Alpha / metal ion binding / DUF1244 domain-containing protein
Function and homology information
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsKim, Y. / Joachimiak, A. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of Protein of Unknown Function (DUF1244) from Sinorhizobium meliloti
Authors: Kim, Y. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: 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_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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE AUTHORS STATE THAT AT SEQUENCE POSITION 16 IT COULD BE EITHER VALINE OR THREONINE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein DUF1244
B: Hypothetical protein DUF1244
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7314
Polymers24,6822
Non-polymers492
Water2,108117
1
A: Hypothetical protein DUF1244
B: Hypothetical protein DUF1244
hetero molecules

A: Hypothetical protein DUF1244
B: Hypothetical protein DUF1244
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4618
Polymers49,3644
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area9820 Å2
ΔGint-95 kcal/mol
Surface area17250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.994, 80.994, 64.708
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypothetical protein DUF1244 / Hypothesis


Mass: 12341.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R02792, SMc04008 / Plasmid: modified pET vector / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q92M60
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M Sodium citrate, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97904 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 6, 2006 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.12→35.07 Å / Num. all: 13992 / Num. obs: 13992 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 6.6
Reflection shellResolution: 2.12→2.2 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.92 / Num. unique all: 1320 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
CCP4phasing
ARP/wARPmodel building
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.12→35.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.522 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.212
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.26288 1382 9.9 %RANDOM
Rwork0.20859 ---
all0.21407 12547 --
obs0.21407 12547 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.415 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20.65 Å20 Å2
2--1.29 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.12→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 2 117 1541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211588
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9412155
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43923.64696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.77115284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9371521
X-RAY DIFFRACTIONr_chiral_restr0.1260.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021298
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.2796
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21114
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1091.5979
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67321536
X-RAY DIFFRACTIONr_scbond_it2.6043692
X-RAY DIFFRACTIONr_scangle_it4.0054.5619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 88 -
Rwork0.256 863 -
obs-863 93.6 %

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