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- PDB-3po0: Crystal structure of SAMP1 from Haloferax volcanii -

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Basic information

Entry
Database: PDB / ID: 3po0
TitleCrystal structure of SAMP1 from Haloferax volcanii
ComponentsSmall archaeal modifier protein 1
KeywordsPROTEIN BINDING / ubiquitin-like protein
Function / homology
Function and homology information


protein modification by small protein conjugation / protein tag activity / nucleotide binding
Similarity search - Function
MoaD, archaeal-type / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Small archaeal modifier protein 1
Similarity search - Component
Biological speciesHaloferax volcanii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJeong, Y.J. / Jeong, B.-C. / Song, H.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of ubiquitin-like small archaeal modifier protein 1 (SAMP1) from Haloferax volcanii.
Authors: Jeong, Y.J. / Jeong, B.-C. / Song, H.K.
History
DepositionNov 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Database references / Structure summary
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small archaeal modifier protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4206
Polymers9,0881
Non-polymers3325
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.881, 42.251, 43.568
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 9087.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax volcanii (archaea) / Strain: DS2 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: D4GUF6
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1242
2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 6C111.23985
SYNCHROTRONPhoton Factory AR-NE3A20.97951, 0.97973, 0.98361
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.239851
20.979511
30.979731
40.983611
ReflectionResolution: 1.55→50 Å / Num. all: 11712 / Num. obs: 11712 / Redundancy: 12.8 % / Rsym value: 0.064

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.55→30.193 Å / SU ML: 0.21 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1124 9.81 %RANDOM
Rwork0.1995 ---
all0.2037 11712 --
obs0.2037 11459 97.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.704 Å2 / ksol: 0.448 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0304 Å2-0 Å20 Å2
2--3.6894 Å20 Å2
3----6.7198 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms639 0 8 89 736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006652
X-RAY DIFFRACTIONf_angle_d0.964886
X-RAY DIFFRACTIONf_dihedral_angle_d10.716222
X-RAY DIFFRACTIONf_chiral_restr0.061100
X-RAY DIFFRACTIONf_plane_restr0.004122
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5502-1.62070.29621180.2771120093
1.6207-1.70620.23721430.224123096
1.7062-1.8130.21241560.1935124297
1.813-1.9530.23531370.1721127798
1.953-2.14950.20161480.1821304100
2.1495-2.46040.22061410.17521325100
2.4604-3.09940.25111370.18731339100
3.0994-30.19880.26721440.21661418100
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)
16.6294-2.4873-4.361.23182.16477.6772-0.09180.09710.05650.0870.0838-0.15840.577-0.15360.02470.1370.0092-0.03410.135-0.03210.1838-5.9493-3.97041.163
20.14510.4674-0.89613.4116-2.75925.5528-0.02120.24160.3327-0.16530.5761.62310.0015-2.5183-0.47310.136-0.1263-0.03720.5770.14150.2792-17.9683-2.97630.9229
38.5795-1.5133-1.04330.6873-0.72692.09660.32330.066-1.1262-0.3211-0.06510.4850.61820.0757-0.14220.23260.0111-0.04730.1553-0.06610.232-8.5286-8.70840.6849
41.0208-1.7685-2.57926.1992.69648.20950.01840.37720.2236-1.06910.8969-1.07640.63970.5197-0.51780.32390.06730.06650.3563-0.14070.34613.1429-3.9697-9.7021
54.37111.46050.46972.9935-0.09662.2255-0.14550.3194-0.055-0.26440.22510.05210.11240.3474-0.08480.1565-0.0162-0.00120.1989-0.01450.1523-5.3223-0.4802-8.6108
61.941-1.24410.54294.5626-6.35959.97110.1930.46020.1877-0.60780.0692-0.07620.446-1.1181-0.25430.1801-0.02660.01150.32520.00970.1891-15.7388-1.7086-7.965
74.00473.8177-2.65575.2266-5.39057.8170.3128-0.3630.44030.6875-0.31630.3218-0.98220.9639-0.15620.19680.05380.04110.21210.00850.1615-14.1578.0374-9.8237
84.80363.55081.95383.55510.1063.5997-0.08890.60470.1417-0.1370.0270.3598-0.0249-0.02960.06180.10740.05330.01890.209-0.03650.1538-12.891110.5402-3.0892
92.6349-1.32482.04576.0756-2.20712.0819-0.04120.0143-0.17160.6021-0.0605-0.0635-0.18540.13880.02240.14050.00940.01870.1352-0.00350.1556-1.20454.69393.437
101.9696-1.05472.0944.0236-3.00153.36640.09540.2162-0.25780.2536-0.22770.0711-0.14930.50170.19510.1472-0.0126-0.00560.17020.01970.18612.41014.6279-3.2519
112.7664-2.39080.41662.0652-0.33051.2231-0.1644-0.1038-0.41350.21320.17890.10070.25580.1598-0.1010.13720.0330.01730.14940.00420.2087-1.9829-1.43071.7982
124.7851-1.4661-4.01569.35335.94559.05380.77910.6060.62270.76261.14340.3491-1.2031-1.4478-0.28370.37460.28450.24480.41650.38710.3282-16.99827.4896.6487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 0:7)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 8:14)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 15:19)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 20:26)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 27:38)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 39:44)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 45:52)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 53:57)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 58:64)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 65:74)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 75:80)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 81:87)

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