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- PDB-3e35: Actinobacteria-specific protein of unknown function, SCO1997 -

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Basic information

Entry
Database: PDB / ID: 3.0E+35
TitleActinobacteria-specific protein of unknown function, SCO1997
ComponentsUncharacterized protein SCO1997
KeywordsUNKNOWN FUNCTION / alpha/beta/alpha Structure / Actinobacteria-Specific protein / Conserved Protein
Function / homology
Function and homology information


Rv2714-like / PAC-like subunit / Helix Hairpins - #100 / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Rv2714-like / PAC-like subunit / Helix Hairpins - #100 / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsGao, B. / Gupta, R.S. / Sugiman-Marangos, S. / Junop, M.S.
CitationJournal: Bmc Struct.Biol. / Year: 2009
Title: Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor.
Authors: Gao, B. / Sugiman-Marangos, S. / Junop, M.S. / Gupta, R.S.
History
DepositionAug 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 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 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein SCO1997
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0693
Polymers36,0201
Non-polymers492
Water4,143230
1
A: Uncharacterized protein SCO1997
hetero molecules

A: Uncharacterized protein SCO1997
hetero molecules

A: Uncharacterized protein SCO1997
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2079
Polymers108,0613
Non-polymers1466
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6920 Å2
ΔGint-28.1 kcal/mol
Surface area36100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.083, 135.083, 135.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-326-

MG

21A-327-

MG

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Components

#1: Protein Uncharacterized protein SCO1997


Mass: 36020.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO1997 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9S2K6
#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


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES pH 6.5, 0.55M Magnesium formate, 1.5% Glycerol, 0.25% N-octyl-beta-D-glucoside, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
PH range: 7.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2007
Details: Pt-coated toroidal Si mirror for horizontal and vertical focusing followed by double flat Si crystal monochromator
RadiationMonochromator: Flat Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 27763 / Num. obs: 27763 / % possible obs: 100 % / Redundancy: 22.1 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 37.98
Reflection shellResolution: 2→2.07 Å / Redundancy: 22.2 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→95.35 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.303 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23401 1010 5 %RANDOM
Rwork0.17458 ---
obs0.17747 19088 95.77 %-
all-25482 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.305 Å2
Refinement stepCycle: LAST / Resolution: 2.2→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 2 230 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0212136
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4221.9542919
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.9855267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76723.714105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58615318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1341517
X-RAY DIFFRACTIONr_chiral_restr0.210.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211675
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2982
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21474
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2199
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0150.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3450.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.31.51340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11922158
X-RAY DIFFRACTIONr_scbond_it3.9873796
X-RAY DIFFRACTIONr_scangle_it5.8954.5761
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 78 -
Rwork0.203 1491 -
obs--99.87 %
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)
12.98990.73141.92072.79861.68925.10250.03440.02340.0833-0.06740.1941-0.44330.10360.6678-0.2286-0.01520.0639-0.02160.1237-0.05220.0559-5.108-36.941-30.191
24.147-0.0496-1.27390.05190.28491.8091-0.04-0.1779-0.4250.34580.0447-0.02470.40760.2241-0.00480.08390.0477-0.04090.0012-0.00030.0341-18.654-41.135-20
34.1312-1.96360.66373.1194-0.47312.79290.0474-0.11630.03120.01090.1027-0.22450.14360.4759-0.1501-0.0930.0221-0.02720.0476-0.0617-0.0406-8.08-34.679-29.147
40.24180.3264-0.07932.92020.44910.8582-0.05420.36120.223-0.68710.16010.0260.01360.4527-0.1060.08720.033-0.00560.1624-0.02960.015-9.435-39.922-46.034
510.2107-1.1555-0.88244.4246-0.42712.17120.03651.5146-0.1141-0.71270.0356-0.3311-0.07670.298-0.07210.1075-0.05490.08050.3106-0.03980.0492-8.447-28.68-45.062
63.44881.4461.60324.9276-0.27295.1950.19070.1541-0.3089-0.23520.2845-0.20210.85860.5538-0.47520.21090.1514-0.09440.0845-0.0704-0.0128-10.101-48.628-44.296
751.424112.304726.149215.16795.597833.43740.80620.2151-1.09630.55230.5353-0.08812.9738-0.1003-1.34150.796-0.0085-0.2017-0.02240.04940.1363-21.304-60.237-48.661
812.83240.0933-0.0998.2553-1.66237.37580.16120.3944-0.5644-0.09650.21540.32861.088-0.4551-0.37670.5224-0.0746-0.20420.09430.0473-0.0136-24.555-51.825-60.878
90.7835-0.1797-0.07380.7340.20261.52010.04850.02280.0153-0.10410.0723-0.09150.21290.2559-0.12080.16940.0397-0.03870.1607-0.00070.1718-11.696-39.739-35.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 53
2X-RAY DIFFRACTION2A54 - 89
3X-RAY DIFFRACTION3A90 - 131
4X-RAY DIFFRACTION4A132 - 161
5X-RAY DIFFRACTION5A162 - 197
6X-RAY DIFFRACTION6A198 - 242
7X-RAY DIFFRACTION7A243 - 255
8X-RAY DIFFRACTION8A256 - 276
9X-RAY DIFFRACTION9A328 - 554

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