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- PDB-2qzi: The crystal structure of a conserved protein of unknown function ... -

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Basic information

Entry
Database: PDB / ID: 2qzi
TitleThe crystal structure of a conserved protein of unknown function from Streptococcus thermophilus LMG 18311.
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC86636 / Streptococcus thermophilus LMG 18311 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyStreptococcus thermophilus LMG 18311 protein like / Streptococcus thermophilus LMG 18311 protein like / Protein of unknown function DUF1827 / LMG 18311 protein-like superfamily / Domain of unknown function (DUF1827) / 3-Layer(aba) Sandwich / Alpha Beta / Cytosolic protein
Function and homology information
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsTan, K. / Zhou, M. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved protein of unknown function from Streptococcus thermophilus LMG 18311.
Authors: Tan, K. / Zhou, M. / Freeman, L. / Joachimiak, A.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / 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_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_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 300BIOMOLECULE: 1, 2, 3, 4 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ...BIOMOLECULE: 1, 2, 3, 4 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN, AND THAT IT IS LIKELY MONOMERIC THOUGH SUPER BETA-SHEET IS FORMED BETWEEN MONOMERS A AND B AS WELL AS C AND D IN THIS CRYSTAL STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,56112
Polymers48,3384
Non-polymers2238
Water2,936163
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1303
Polymers12,0841
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2155
Polymers12,0841
Non-polymers1314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1303
Polymers12,0841
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,0841
Polymers12,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.783, 150.783, 103.247
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsExperimentally unknown. From molecular packing, it is likely monomeric.

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Components

#1: Protein
Uncharacterized protein


Mass: 12084.452 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Strain: LMG 18311 / Gene: stu0600 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5M594
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.5 Å3/Da / Density % sol: 64.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 35% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.2→36.23 Å / Num. all: 35201 / Num. obs: 35201 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 54.3
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2143 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→36.23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.53 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.203 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25112 1755 5 %RANDOM
Rwork0.21025 ---
all0.21229 33315 --
obs0.21229 33315 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0.4 Å20 Å2
2---0.81 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 11 163 3472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223423
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9474655
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4825415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2425.029171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.65515646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3471517
X-RAY DIFFRACTIONr_chiral_restr0.1690.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022527
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.21467
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22256
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2205
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9991.52036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7623359
X-RAY DIFFRACTIONr_scbond_it3.08931415
X-RAY DIFFRACTIONr_scangle_it4.7884.51287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 121 -
Rwork0.224 2155 -
obs-2276 88.73 %
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)
14.18860.5962-1.33113.91610.94453.77610.10850.09720.1617-0.3870.08130.122-0.4002-0.0649-0.1898-0.2855-0.0627-0.0217-0.4077-0.0754-0.7401-53.43230.021-1.86
23.00650.3131-0.21243.14980.41313.3309-0.08010.24620.0624-0.15070.0620.0573-0.1617-0.02610.0181-0.3424-0.06790.0164-0.4357-0.0528-0.7286-47.57451.40716.73
34.44130.1630.66433.65471.11382.69580.05770.4755-0.2365-0.28910.1222-0.17830.07110.3388-0.1798-0.3259-0.0737-0.0253-0.1944-0.0948-0.6516-18.80949.17411.982
47.31780.31742.357615.3092.79973.9958-0.2330.4479-0.8392-0.43370.8212-1.44690.36490.6409-0.5882-0.06220.0093-0.1971-0.0396-0.43760.0876-25.3223.6550.588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1003 - 103
2X-RAY DIFFRACTION2BB0 - 1003 - 103
3X-RAY DIFFRACTION3CC0 - 1003 - 103
4X-RAY DIFFRACTION4DD3 - 1006 - 103

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