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- PDB-3dt5: C_terminal domain of protein of unknown function AF_0924 from Arc... -

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Basic information

Entry
Database: PDB / ID: 3dt5
TitleC_terminal domain of protein of unknown function AF_0924 from Archaeoglobus fulgidus.
ComponentsUncharacterized protein AF_0924
Keywordsstructural genomics / unknown function / APC7732 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Membrane / Transmembrane
Function / homologyAF_0924 fold / AF_0924 domain / : / Uncharacterized protein AF_0924 / Orthogonal Bundle / Mainly Alpha / plasma membrane / Uncharacterized protein AF_0924
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsOsipiuk, J. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of C_terminal domain of protein of unknown function AF_0924 from Archaeoglobus fulgidus.
Authors: OSIPIUK, J. / EVDOKIMOVA, E. / KUDRITSKA, M. / SAVCHENKO, A. / EDWARDS, A.M. / JOACHIMIAK, A.
History
DepositionJul 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 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 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein AF_0924
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1513
Polymers16,0491
Non-polymers1022
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)65.413, 65.413, 76.582
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

Detailsauthors state that putative biological unit is the same as asymmetric unit.

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Components

#1: Protein Uncharacterized protein AF_0924


Mass: 16048.986 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_0924 / Plasmid: pET15b modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O29338
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M calcium chloride, 25% PEG 5500 MME, 0.1 M Bis-Tris buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 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: 1.94→50 Å / Num. all: 12898 / Num. obs: 12898 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.6 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.293 / Net I/σ(I): 13
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 23.3 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 4.18 / Num. unique all: 634 / Χ2: 0.884 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.94→33 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.881 / SU B: 5.352 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 626 4.9 %RANDOM
Rwork0.169 ---
all0.171 12850 --
obs0.171 12850 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.78 Å2 / Biso mean: 42.192 Å2 / Biso min: 25.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.94→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 5 89 1097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221080
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9671469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3725132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.59224.18255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24415201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.669156
X-RAY DIFFRACTIONr_chiral_restr0.1260.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02821
X-RAY DIFFRACTIONr_nbd_refined0.2260.2466
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.273
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1930.21
X-RAY DIFFRACTIONr_mcbond_it1.0551.5636
X-RAY DIFFRACTIONr_mcangle_it1.71921002
X-RAY DIFFRACTIONr_scbond_it2.6543525
X-RAY DIFFRACTIONr_scangle_it4.214.5460
LS refinement shellResolution: 1.939→1.989 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 35 -
Rwork0.21 888 -
all-923 -
obs-923 100 %
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)
16.577810.5485-0.423829.775-1.864113.0781-0.06460.0505-0.66630.4176-0.0185-3.18621.10811.15440.0831-0.03190.0136-0.0710.0533-0.03140.156229.944717.736812.9412
20.603-1.8104-0.16356.31260.21530.13110.0020.04430.04370.3640.068-0.32340.0491-0.0028-0.07-0.0539-0.0043-0.0385-0.1115-0.01-0.071820.152231.303315.7684
30.8495-2.7999-1.53619.24715.24894.6235-0.0280.0033-0.0039-0.11680.1061-0.42980.00310.0785-0.0782-0.0904-0.00960.009-0.1261-0.0134-0.059521.551736.81747.2711
43.28262.06040.97095.47-0.03020.38510.32250.09960.0217-0.0673-0.1521-0.2038-0.0122-0.0766-0.1704-0.0590.01630.0156-0.0885-0.0003-0.102721.697326.71693.8653
53.57564.2653-0.19735.1094-0.11460.69480.27710.0990.16430.1057-0.07660.00510.20440.0249-0.2004-0.0835-0.01560.0064-0.08140.0013-0.072119.92117.41755.8623
63.0982-1.86781.56331.1262-0.91559.7030.1722-0.0333-0.1070.2806-0.12890.09880.09220.013-0.0433-0.1067-0.0328-0.0051-0.0968-0.0127-0.051612.368919.80855.3423
77.9257-0.8271.71914.621-3.47531.12020.28840.3374-0.5637-0.9045-0.2071-0.43490.359-0.0039-0.08120.0171-0.0173-0.0448-0.06430.0096-0.085112.9235.36173.6346
80.72381.29620.79852.44561.00172.3534-0.0629-0.05670.1280.12910.04340.22080.0621-0.04460.0195-0.10570.0271-0.0003-0.1111-0.0046-0.059410.471240.800813.2055
94.102-3.4790.853311.695-3.25120.908-0.18830.0937-0.2994-0.25870.32290.33760.3275-0.4896-0.1346-0.1307-0.0550.0013-0.0284-0.0497-0.07145.698629.2329.8484
100.25230.0168-0.13462.61730.84393.04070.0453-0.0790.13230.2502-0.08910.04110.3595-0.25640.0439-0.0085-0.03950.0059-0.12960.0031-0.10614.909419.728816.8227
118.87140.8013-0.53066.99960.05781.76810.0534-0.33880.13290.67580.132-0.4057-0.1164-0.0498-0.18540.0051-0.0316-0.1001-0.1097-0.0117-0.115824.252212.054119.5328
1256.4949-10.659141.092123.2512-7.976829.891-1.5257-6.58221.71014.95642.5395-0.79010.061-3.174-1.01381.11730.0263-0.10120.96330.14250.548127.18512.046527.0384
136.2131-0.66792.173114.5244-5.504814.1291-0.2596-0.2501-0.17030.46850.21550.59340.1171-0.49780.0441-0.0124-0.10940.0901-0.0838-0.0523-0.116510.389129.380220.3273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA77 - 8715 - 25
2X-RAY DIFFRACTION2AA88 - 10226 - 40
3X-RAY DIFFRACTION3AA103 - 11041 - 48
4X-RAY DIFFRACTION4AA111 - 11749 - 55
5X-RAY DIFFRACTION5AA118 - 12356 - 61
6X-RAY DIFFRACTION6AA124 - 12862 - 66
7X-RAY DIFFRACTION7AA129 - 13767 - 75
8X-RAY DIFFRACTION8AA138 - 14976 - 87
9X-RAY DIFFRACTION9AA150 - 16088 - 98
10X-RAY DIFFRACTION10AA161 - 16899 - 106
11X-RAY DIFFRACTION11AA169 - 177107 - 115
12X-RAY DIFFRACTION12AA178 - 183116 - 121
13X-RAY DIFFRACTION13AA184 - 195122 - 133

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