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- PDB-2ra9: Crystal structure of a duf1285 family protein (sbal_2486) from sh... -

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Basic information

Entry
Database: PDB / ID: 2ra9
TitleCrystal structure of a duf1285 family protein (sbal_2486) from shewanella baltica os155 at 1.40 A resolution
ComponentsUncharacterized protein DUF1285
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


duf1285 protein / duf1285 like domain / Protein of unknown function DUF1285 / DUF1285, beta-roll domain superfamily / Domain of unknown function (DUF1285), N-terminal domain / duf1285 like fold / duf1285 protein fold / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesShewanella baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.
Authors: Han, G.W. / Bakolitsa, C. / Miller, M.D. / Kumar, A. / Carlton, D. / Najmanovich, R.J. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, ...Authors: Han, G.W. / Bakolitsa, C. / Miller, M.D. / Kumar, A. / Carlton, D. / Najmanovich, R.J. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ernst, D. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Jaroszewski, L. / Jin, K.K. / Johnson, H.A. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Marciano, D. / McMullan, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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.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.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_type.id / _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 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 RESIDUES 9-157 OF THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein DUF1285
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3779
Polymers16,9201
Non-polymers4578
Water4,161231
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.409, 62.286, 73.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein DUF1285


Mass: 16920.020 Da / Num. of mol.: 1 / Fragment: Residues 9-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella baltica (bacteria) / Strain: OS155 / Gene: YP_001050848.1, Sbal_2486 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3D5G6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: NANODROP, 20.0% Isopropanol, 20.0% PEG 4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795, 0.9798, 1.0000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
311
ReflectionResolution: 1.4→29.854 Å / Num. obs: 35222 / % possible obs: 99.6 % / Observed criterion σ(I): -4 / Redundancy: 4.9 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.444.60.6131.31161325460.61398.5
1.44-1.484.80.4831.61199425060.48399.3
1.48-1.524.90.3492.21176823950.34999.5
1.52-1.5750.3052.51176023660.305100
1.57-1.6250.233.31159323040.2399.9
1.62-1.6750.1794.31131222490.179100
1.67-1.745.10.14951088621510.149100
1.74-1.8150.126.11046120750.1299.9
1.81-1.8950.0927.51006620110.092100
1.89-1.9850.0758.8957619050.07599.9
1.98-2.0950.06310.2915018210.06399.9
2.09-2.2150.05611.8864817340.05699.9
2.21-2.374.90.05511.2811316460.05599.9
2.37-2.564.90.05112.6747315140.05199.8
2.56-2.84.80.05111.7675714070.05199.6
2.8-3.134.60.05112590112760.05199.7
3.13-3.614.30.04413.7490511440.04499.6
3.61-4.4350.03518.249489810.035100
4.43-6.2650.03318.938737710.03398.9
6.26-29.8544.70.03717.419664200.03793.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHARPphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→29.854 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.765 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.055
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 4. RESIDUES AT THE N-TERMINUS (0, 9-28) ARE DISORDERED AND WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1764 5 %RANDOM
Rwork0.162 ---
obs0.164 35168 99.43 %-
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: 13.495 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 29 231 1278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221081
X-RAY DIFFRACTIONr_bond_other_d0.0040.02731
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9761463
X-RAY DIFFRACTIONr_angle_other_deg0.93631788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.71724.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12615177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.076154
X-RAY DIFFRACTIONr_chiral_restr0.1040.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02212
X-RAY DIFFRACTIONr_nbd_refined0.240.2225
X-RAY DIFFRACTIONr_nbd_other0.210.2758
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2514
X-RAY DIFFRACTIONr_nbtor_other0.0830.2552
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2154
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1580.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.215
X-RAY DIFFRACTIONr_mcbond_it2.4793643
X-RAY DIFFRACTIONr_mcbond_other1.5283256
X-RAY DIFFRACTIONr_mcangle_it3.44551047
X-RAY DIFFRACTIONr_scbond_it4.6348450
X-RAY DIFFRACTIONr_scangle_it6.29811413
X-RAY DIFFRACTIONr_rigid_bond_restr2.62931897
X-RAY DIFFRACTIONr_sphericity_free5.7613232
X-RAY DIFFRACTIONr_sphericity_bonded3.85231791
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 139 -
Rwork0.21 2401 -
all-2540 -
obs--98.07 %

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