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- PDB-3s3t: Universal stress protein UspA from Lactobacillus plantarum -

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Basic information

Entry
Database: PDB / ID: 3s3t
TitleUniversal stress protein UspA from Lactobacillus plantarum
ComponentsNucleotide-binding protein, universal stress protein UspA family
KeywordsCHAPERONE / structural genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / nucleotide-binding protein / Unknown function
Function / homology
Function and homology information


ATP binding / cytoplasm
Similarity search - Function
Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / Universal stress protein / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOsipiuk, J. / Li, H. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Universal stress protein UspA from Lactobacillus plantarum.
Authors: Osipiuk, J. / Li, H. / Cobb, G. / Joachimiak, A.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleotide-binding protein, universal stress protein UspA family
B: Nucleotide-binding protein, universal stress protein UspA family
C: Nucleotide-binding protein, universal stress protein UspA family
D: Nucleotide-binding protein, universal stress protein UspA family
E: Nucleotide-binding protein, universal stress protein UspA family
F: Nucleotide-binding protein, universal stress protein UspA family
G: Nucleotide-binding protein, universal stress protein UspA family
H: Nucleotide-binding protein, universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,66533
Polymers126,4918
Non-polymers5,17425
Water15,961886
1
A: Nucleotide-binding protein, universal stress protein UspA family
B: Nucleotide-binding protein, universal stress protein UspA family
C: Nucleotide-binding protein, universal stress protein UspA family
D: Nucleotide-binding protein, universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,80316
Polymers63,2464
Non-polymers2,55712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13660 Å2
ΔGint-90 kcal/mol
Surface area22510 Å2
MethodPISA
2
A: Nucleotide-binding protein, universal stress protein UspA family
C: Nucleotide-binding protein, universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9028
Polymers31,6232
Non-polymers1,2796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-44 kcal/mol
Surface area13360 Å2
MethodPISA
3
B: Nucleotide-binding protein, universal stress protein UspA family
D: Nucleotide-binding protein, universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9028
Polymers31,6232
Non-polymers1,2796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-46 kcal/mol
Surface area13230 Å2
MethodPISA
4
E: Nucleotide-binding protein, universal stress protein UspA family
F: Nucleotide-binding protein, universal stress protein UspA family
G: Nucleotide-binding protein, universal stress protein UspA family
H: Nucleotide-binding protein, universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,86217
Polymers63,2464
Non-polymers2,61613
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13880 Å2
ΔGint-88 kcal/mol
Surface area22180 Å2
MethodPISA
5
E: Nucleotide-binding protein, universal stress protein UspA family
G: Nucleotide-binding protein, universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9619
Polymers31,6232
Non-polymers1,3387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-44 kcal/mol
Surface area13170 Å2
MethodPISA
6
F: Nucleotide-binding protein, universal stress protein UspA family
H: Nucleotide-binding protein, universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9028
Polymers31,6232
Non-polymers1,2796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-42 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.015, 56.187, 109.144
Angle α, β, γ (deg.)102.130, 100.530, 90.360
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Nucleotide-binding protein, universal stress protein UspA family


Mass: 15811.425 Da / Num. of mol.: 8 / Fragment: sequence database residues 4-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: lp_1163 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88XN4, UniProt: F9UMW3*PLUS

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Non-polymers , 5 types, 911 molecules

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M calcium acetate, 0.1 M Tris buffer, 20% PEG-3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 11, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→32.5 Å / Num. all: 81926 / Num. obs: 81926 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.257 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.936.10.5612.8527290.87862
1.93-1.975.90.42731930.8571.8
1.97-2.015.80.32339580.78989.6
2.01-2.056.30.27742440.79396.5
2.05-2.096.40.23142130.84396.3
2.09-2.146.40.21143360.83496.7
2.14-2.196.40.18441780.89196.4
2.19-2.256.30.16843330.95997
2.25-2.326.30.15842850.95997
2.32-2.396.30.13141980.98196.9
2.39-2.486.30.12342871.03696.7
2.48-2.586.30.11143151.15897.1
2.58-2.76.20.142301.23796.8
2.7-2.846.20.08743121.36597.3
2.84-3.026.20.07542541.42197.1
3.02-3.256.20.06543051.56796.9
3.25-3.586.10.05642281.72496.4
3.58-4.096.10.05141971.89794.7
4.09-5.165.70.04640232.04791.7
5.16-506.30.04641082.8593.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZSK

2zsk


Resolution: 1.9→32.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.543 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 4103 5 %RANDOM
Rwork0.1684 ---
all0.171 81918 --
obs0.171 81918 92.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.14 Å2 / Biso mean: 29.2979 Å2 / Biso min: 10.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.34 Å20.73 Å2
2---0.72 Å2-1.67 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8800 0 308 886 9994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0219605
X-RAY DIFFRACTIONr_bond_other_d0.0010.025993
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.97913280
X-RAY DIFFRACTIONr_angle_other_deg0.955314799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2251247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21824.633436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.237151435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4521556
X-RAY DIFFRACTIONr_chiral_restr0.0930.21571
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021795
X-RAY DIFFRACTIONr_mcbond_it0.7981.55968
X-RAY DIFFRACTIONr_mcbond_other0.2561.52323
X-RAY DIFFRACTIONr_mcangle_it1.34429751
X-RAY DIFFRACTIONr_scbond_it2.18633637
X-RAY DIFFRACTIONr_scangle_it3.374.53478
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 197 -
Rwork0.268 3867 -
all-4064 -
obs-4064 62.04 %
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)
11.8109-0.6253-0.2560.8680.38360.76820.0046-0.25810.10990.03880.0773-0.1303-0.01410.071-0.08190.0621-0.03520.01880.0697-0.02530.03439.92645.005917.1502
20.79120.65940.54080.94080.91691.2433-0.0645-0.05970.1315-0.2233-0.00270.1296-0.4444-0.10520.06720.22520.05220.00640.05470.01850.0915-10.258917.33280.901
31.04510.43810.66080.75380.31051.11270.12010.15-0.24980.05060.081-0.09770.06510.1016-0.20110.01570.0112-0.02480.0449-0.03960.099813.1348-15.165-4.4648
41.55360.1034-0.05490.95940.41791.0496-0.01290.1701-0.019-0.04570.04860.0607-0.0444-0.0582-0.03580.0144-0.017-0.02090.04780.03420.048-12.9916-7.967-14.3174
52.1572-0.1701-0.89340.45970.34580.87050.0290.2637-0.3017-0.0128-0.116-0.00790.1022-0.170.0870.11650.0152-0.00850.0563-0.03780.0727-17.0304-28.281545.0713
60.95530.12570.34450.8242-0.24791.30070.04630.14570.0513-0.2373-0.157-0.17770.01740.0810.11070.15430.09610.07860.0870.06670.06093.0289-10.31235.1108
71.73050.6790.39421.03810.4040.85980.0697-0.3010.15630.0203-0.15680.05630.081-0.1280.08720.0186-0.01430.01580.0887-0.0360.0395-20.3348-10.251868.1583
81.6373-0.1363-0.38930.58970.37472.0370.0182-0.04740.2469-0.0724-0.0637-0.1363-0.06950.1670.04540.0265-0.0062-0.01790.03880.04720.13865.77711.128362.1883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 146
2X-RAY DIFFRACTION2B3 - 146
3X-RAY DIFFRACTION3C2 - 146
4X-RAY DIFFRACTION4D2 - 146
5X-RAY DIFFRACTION5E2 - 146
6X-RAY DIFFRACTION6F3 - 146
7X-RAY DIFFRACTION7G3 - 146
8X-RAY DIFFRACTION8H3 - 146

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