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- PDB-3qtb: Structure of the universal stress protein from Archaeoglobus fulg... -

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Basic information

Entry
Database: PDB / ID: 3qtb
TitleStructure of the universal stress protein from Archaeoglobus fulgidus in complex with dAMP
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG / a/b class / RFM like / putative universal stress protein
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 / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / UspA domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTkaczuk, K.L. / Shumilin, I.A. / Chruszcz, M. / Cymborowski, M. / Xu, X. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Evol Appl / Year: 2013
Title: Structural and functional insight into the universal stress protein family.
Authors: Tkaczuk, K.L. / Shumilin, I.A. / Chruszcz, M. / Evdokimova, E. / Savchenko, A. / Minor, W.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Jun 26, 2013Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.6Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.8Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,1876
Polymers34,6792
Non-polymers5084
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-7 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.607, 42.655, 61.289
Angle α, β, γ (deg.)90.00, 116.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 17339.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0826 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: O29432
#2: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.84 Å3/Da / Density % sol: 33.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M ammonium sulfate, 0.1M BIS-TRIS pH 5.5, 25%w/v polyethylene glycol, 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 14965 / Num. obs: 14965 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 21.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.5 / Num. unique all: 734 / Rsym value: 0.405 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.6.0070refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DLO

3dlo
PDB Unreleased entry


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.228 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.254 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23747 738 5 %RANDOM
Rwork0.1997 ---
all0.2017 14059 --
obs0.2017 14059 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-1.35 Å2
2--0.63 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 34 50 2054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222031
X-RAY DIFFRACTIONr_bond_other_d0.0060.021394
X-RAY DIFFRACTIONr_angle_refined_deg1.4252.0032750
X-RAY DIFFRACTIONr_angle_other_deg0.8433402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46923.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15815355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6621519
X-RAY DIFFRACTIONr_chiral_restr0.0810.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 54 -
Rwork0.196 1027 -
obs--99.45 %
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)
12.86960.7256-0.87631.2427-0.36331.3092-0.0394-0.0858-0.01440.01490.06710.0196-0.03440.1352-0.02760.0740.0267-0.02190.0374-0.00780.052419.754629.7929-13.3028
26.8741-6.571-1.89810.17586.460313.78420.3150.4575-0.0253-0.3762-0.1049-0.2151-0.03720.196-0.21020.07660.0188-0.00070.1751-0.03430.127829.266823.4723-29.6174
33.20470.9418-1.67011.7717-0.12961.0569-0.09-0.1662-0.2530.07930.0851-0.0850.12080.18920.00480.16850.0141-0.0310.1739-0.02820.19624.164323.0176-15.2641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 104
2X-RAY DIFFRACTION1B1 - 102
3X-RAY DIFFRACTION2B103 - 116
4X-RAY DIFFRACTION3A116 - 134
5X-RAY DIFFRACTION3B117 - 134

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