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- PDB-3nkg: Crystal Structure of GEBA250068378 from Sulfurospirillum deleyianum -

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Basic information

Entry
Database: PDB / ID: 3nkg
TitleCrystal Structure of GEBA250068378 from Sulfurospirillum deleyianum
Componentsuncharacterized protein GEBA250068378
Keywordsstructural genomics / unknown function / GEBA target / bata-fold / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyJelly Rolls - #790 / Domain of unknown function DUF5625 / Domain of unknown function (DUF5625) / Jelly Rolls / Sandwich / Mainly Beta / ACETIC ACID / DUF5625 domain-containing protein
Function and homology information
Biological speciesSulfurospirillum deleyianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKim, Y. / Marshall, N. / Cobb, G. / Eisen, J. / Kerfeld, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2010
Title: Crystal Structure of GEBA250068378 from Sulfurospirillum deleyianum
Authors: Kim, Y. / Marshall, N. / Cobb, G. / Eisen, J. / Kerfeld, C. / Joachimiak, A.
History
DepositionJun 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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_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_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: uncharacterized protein GEBA250068378
B: uncharacterized protein GEBA250068378
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,35910
Polymers39,7822
Non-polymers5778
Water5,296294
1
A: uncharacterized protein GEBA250068378
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2556
Polymers19,8911
Non-polymers3645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein GEBA250068378
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1034
Polymers19,8911
Non-polymers2123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.373, 39.414, 88.575
Angle α, β, γ (deg.)90.00, 95.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein uncharacterized protein GEBA250068378


Mass: 19891.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurospirillum deleyianum (bacteria) / Strain: DSM 6946 / Gene: Sdel_1248 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D1B2F0
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16 M Magnesium Acetate 0.08 M Sodium Cacodylate pH 6.5, 16% PEG 8000, 20% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 25082 / Num. obs: 25082 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 24.61 Å2 / Rsym value: 0.086 / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→44.087 Å / SU ML: 0.2 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2000 8.2 %random
Rwork0.169 ---
all0.172 24384 --
obs0.172 24384 96.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.507 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 35.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.609 Å2-0 Å24.6817 Å2
2---2.1852 Å20 Å2
3----4.4238 Å2
Refinement stepCycle: LAST / Resolution: 2→44.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 38 294 3054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012894
X-RAY DIFFRACTIONf_angle_d1.23908
X-RAY DIFFRACTIONf_dihedral_angle_d16.4161072
X-RAY DIFFRACTIONf_chiral_restr0.085421
X-RAY DIFFRACTIONf_plane_restr0.005511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0001-2.07160.27051820.22222035221788
2.0716-2.15450.2661920.19182147233994
2.1545-2.25260.23391930.17382169236296
2.2526-2.37130.22992000.17142240244097
2.3713-2.51990.2392000.16942225242598
2.5199-2.71440.22532000.17322240244098
2.7144-2.98750.23452050.18132296250199
2.9875-3.41970.19572060.16542305251199
3.4197-4.30790.17582080.144523342542100
4.3079-44.09780.19642140.15652393260799
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)
11.38910.5322-0.57980.3134-0.36020.46960.00210.0033-0.0394-0.0565-0.0184-0.04970.13870.01620.03830.24790.01890.00750.1313-0.00690.13248.631927.36862.3175
20.1821-0.32620.39530.9961-0.36981.2184-0.04260.00120.1009-0.0605-0.0302-0.06690.123-0.05940.06110.1286-0.02940.01990.1521-0.02040.168421.8328.236835.0252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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