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- PDB-4hrs: Crystal structure of H. volcanii small archaeal modifier protein 2 -

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Basic information

Entry
Database: PDB / ID: 4hrs
TitleCrystal structure of H. volcanii small archaeal modifier protein 2
ComponentsSmall archaeal modifier protein 2
KeywordsPROTEIN BINDING / beta-grasp fold / beta-hinge motif / small ubiquitin-like modifier
Function / homology
Function and homology information


protein modification by small protein conjugation / protein tag activity / nucleotide binding
Similarity search - Function
: / : / : / Small archaeal modifier protein 2 / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Small archaeal modifier protein 2
Similarity search - Component
Biological speciesHaloferax volcanii DS2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHao, B.
CitationJournal: Protein Sci. / Year: 2013
Title: Crystal structure of the ubiquitin-like small archaeal modifier protein 2 from Haloferax volcanii.
Authors: Li, Y. / Maciejewski, M.W. / Martin, J. / Jin, K. / Zhang, Y. / Maupin-Furlow, J.A. / Hao, B.
History
DepositionOct 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Small archaeal modifier protein 2


Theoretical massNumber of molelcules
Total (without water)7,2081
Polymers7,2081
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Small archaeal modifier protein 2

A: Small archaeal modifier protein 2


Theoretical massNumber of molelcules
Total (without water)14,4162
Polymers14,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3470 Å2
ΔGint-16 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.605, 64.603, 104.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Small archaeal modifier protein 2 / SAMP 2 / Ubiquitin-like small archaeal modifier protein 2


Mass: 7207.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax volcanii DS2 (archaea) / Strain: DS70 / Gene: HVO_0202 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D4GZE7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM bis-tris-propane-HCl (pH 6.8), 25-30% (w/v) PEG 400, 0.2 M MgCl2, 0.1 M KCl, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2010 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.01→54.96 Å / Num. all: 5845 / Num. obs: 5594 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 43.4
Reflection shellResolution: 2.01→2.04 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 6.3 / Num. unique all: 239 / Rsym value: 0.293 / % possible all: 97.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CS-Rosetta model

Resolution: 2.3→54.96 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.87 / SU ML: 0.139 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25365 186 4.7 %RANDOM
Rwork0.21488 ---
all0.255 3825 --
obs0.21682 3771 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.593 Å2
Baniso -1Baniso -2Baniso -3
1--24.18 Å20 Å20 Å2
2--41.49 Å20 Å2
3----17.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→54.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms482 0 0 34 516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022498
X-RAY DIFFRACTIONr_bond_other_d0.0020.02318
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.982682
X-RAY DIFFRACTIONr_angle_other_deg0.8483783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.874567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3052420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4641580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.362155
X-RAY DIFFRACTIONr_chiral_restr0.0660.288
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021563
X-RAY DIFFRACTIONr_gen_planes_other00.0290
X-RAY DIFFRACTIONr_mcbond_it1.5883333
X-RAY DIFFRACTIONr_mcbond_other0.2733135
X-RAY DIFFRACTIONr_mcangle_it3.1575544
X-RAY DIFFRACTIONr_scbond_it4.8848165
X-RAY DIFFRACTIONr_scangle_it8.05811138
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.529 13 -
Rwork0.242 255 -
obs-255 97.45 %
Refinement TLS params.Method: refined / Origin x: 9.5391 Å / Origin y: 26.8931 Å / Origin z: 14.9536 Å
111213212223313233
T0.0895 Å20.0178 Å20.0003 Å2-0.1685 Å20.03 Å2---0.0098 Å2
L1.0896 °20.4866 °20.3713 °2-2.1591 °20.4262 °2--0.3239 °2
S0.0608 Å °-0.0267 Å °-0.0335 Å °-0.0944 Å °-0.0828 Å °0.0672 Å °-0.0188 Å °-0.0382 Å °0.022 Å °

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