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- PDB-3fg9: The crystal structure of an universal stress protein UspA family ... -

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Basic information

Entry
Database: PDB / ID: 3fg9
TitleThe crystal structure of an universal stress protein UspA family protein from Lactobacillus plantarum WCFS1
Componentsprotein of universal stress protein UspA family
Keywordsstructural genomics / unknown function / APC60691 / universal stress protein UspA family / nucleotide-binding / Lactobacillus plantarum WCFS1 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


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 / FORMIC ACID / Nucleotide-binding protein, universal stress protein UspA family / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsTan, K. / Li, H. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of an universal stress protein UspA family protein from Lactobacillus plantarum WCFS1
Authors: Tan, K. / Li, H. / Cobb, G. / Joachimiak, A.
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_conn_angle / struct_conn / 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_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: protein of universal stress protein UspA family
B: protein of universal stress protein UspA family
C: protein of universal stress protein UspA family
D: protein of universal stress protein UspA family
E: protein of universal stress protein UspA family
F: protein of universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,57821
Polymers105,0266
Non-polymers55115
Water16,988943
1
A: protein of universal stress protein UspA family
B: protein of universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1967
Polymers35,0092
Non-polymers1875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-23 kcal/mol
Surface area13950 Å2
MethodPISA
2
C: protein of universal stress protein UspA family
D: protein of universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3019
Polymers35,0092
Non-polymers2927
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-18 kcal/mol
Surface area14320 Å2
MethodPISA
3
E: protein of universal stress protein UspA family
F: protein of universal stress protein UspA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0825
Polymers35,0092
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-15 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.355, 118.949, 191.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. It is predicted that chains A and B, C and D, E and F form dimers respectively.

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Components

#1: Protein
protein of universal stress protein UspA family


Mass: 17504.408 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Gene: Lactobacillus plantarum, lp_3663 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q88RY8, UniProt: F9ULL0*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 943 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2M MgActate. 20% PEG3350, 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: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2008 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.47→37.6 Å / Num. all: 149737 / Num. obs: 149737 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 46.3
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.6 / Num. unique all: 6828 / % possible all: 92.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→37.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.301 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.092 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21235 7512 5 %RANDOM
Rwork0.17732 ---
all0.17907 142022 --
obs0.17907 142022 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.47→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7237 0 11 964 8212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227414
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.98410134
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59124.689354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.977151323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7141559
X-RAY DIFFRACTIONr_chiral_restr0.0970.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215653
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3641.54628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09427592
X-RAY DIFFRACTIONr_scbond_it3.08332786
X-RAY DIFFRACTIONr_scangle_it4.7584.52496
X-RAY DIFFRACTIONr_rigid_bond_restr1.70937414
X-RAY DIFFRACTIONr_sphericity_free5.9683959
X-RAY DIFFRACTIONr_sphericity_bonded3.92637262
LS refinement shellResolution: 1.471→1.509 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 559 -
Rwork0.233 9839 -
obs-10398 95.27 %

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