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- PDB-3ush: Crystal Structure of the Q2S0R5 protein from Salinibacter ruber, ... -

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Basic information

Entry
Database: PDB / ID: 3ush
TitleCrystal Structure of the Q2S0R5 protein from Salinibacter ruber, Northeast Structural Genomics Consortium Target SrR207
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / DUF2237 / PF09996 / PSI-Biology / NESG / Northeast Structural Genomics Consortium
Function / homologyProtein of unknown function DUF2237 / Protein of unknown function DUF2237 / Uncharacterized protein conserved in bacteria (DUF2237) / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 2-Layer Sandwich / Alpha Beta / BROMIDE ION / DUF2237 domain-containing protein
Function and homology information
Biological speciesSalinibacter ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.692 Å
AuthorsVorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Q2S0R5 protein from Salinibacter ruber, Northeast Structural Genomics Consortium Target SrR207
Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionNov 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,2155
Polymers28,9752
Non-polymers2403
Water3,279182
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6473
Polymers14,4871
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5672
Polymers14,4871
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.079, 85.417, 42.800
Angle α, β, γ (deg.)90.000, 94.420, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer,15.26 kD,96.4%

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Components

#1: Protein Uncharacterized protein


Mass: 14487.461 Da / Num. of mol.: 2 / Fragment: UNP residues 6-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinibacter ruber (bacteria) / Strain: DSM 13855 / M31 / Gene: SRU_2110 / Plasmid: SrR207-6-125-21.4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q2S0R5
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 37.08 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 6
Details: 40% PEG 400, 0.1M potassium bromide, 0.1M MES, pH 6.0, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 48893 / Num. obs: 48111 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.64 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 4.4 / Num. unique all: 4897 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.692→30.987 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2431 5.06 %RANDOM
Rwork0.171 ---
obs0.172 48059 97.95 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.235 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 72.51 Å2 / Biso mean: 24.533 Å2 / Biso min: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å20 Å20.382 Å2
2---0.714 Å20 Å2
3---3.854 Å2
Refinement stepCycle: LAST / Resolution: 1.692→30.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 3 182 1983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071841
X-RAY DIFFRACTIONf_angle_d1.4022495
X-RAY DIFFRACTIONf_chiral_restr0.097272
X-RAY DIFFRACTIONf_plane_restr0.007335
X-RAY DIFFRACTIONf_dihedral_angle_d13.272679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.692-1.7260.2121180.1832523264189
1.726-1.7640.2181280.1722669279799
1.764-1.8050.1921170.1682699281697
1.805-1.850.2051530.1642687284099
1.85-1.90.1761330.1592692282599
1.9-1.9560.2061330.1632795292898
1.956-2.0190.1561420.162657279999
2.019-2.0910.1921540.162663281799
2.091-2.1750.1541350.1532742287799
2.175-2.2740.1641530.1562719287299
2.274-2.3940.1671380.1522751288999
2.394-2.5430.2031630.16226712834100
2.543-2.740.1961550.1827172872100
2.74-3.0150.2371470.18627442891100
3.015-3.4510.1841550.16827282883100
3.451-4.3460.1771500.1622672282298
4.346-30.9920.2291570.2042499265692
Refinement TLS params.

S33: 0 Å ° / T12: 0.0074 Å2 / 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 °)T11 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83090.12080.09720.9822-0.20180.63570.04230.04220.0556-0.0255-0.0230.01460.03120.03320.0719-0.0070.06560.00880.06659.86141.983628.1301
21.05340.5123-0.37850.8272-0.17540.59640.05690.0132-0.0175-0.009-0.0956-0.0484-0.00750.05320.06160.00430.06970.00780.0668-4.764318.745137.6088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA6 - 123
2X-RAY DIFFRACTION2chain BB6 - 125

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