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- PDB-1y88: Crystal Structure of Protein of Unknown Function AF1548 -

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Basic information

Entry
Database: PDB / ID: 1y88
TitleCrystal Structure of Protein of Unknown Function AF1548
ComponentsHypothetical protein AF1548
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF1548 / APC5567 / Protein Structure Initiative / PSI / Midwest Center for Structural Genomics Center / MCSG
Function / homology
Function and homology information


DNA restriction-modification system / endonuclease activity / nucleotide binding / DNA binding
Similarity search - Function
: / AF1548-like, C-terminal / Restriction endonuclease type IV, Mrr / Restriction endonuclease / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / DNA repair Rad51/transcription factor NusA, alpha-helical / 5' to 3' exonuclease, C-terminal subdomain ...: / AF1548-like, C-terminal / Restriction endonuclease type IV, Mrr / Restriction endonuclease / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / DNA repair Rad51/transcription factor NusA, alpha-helical / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein AF_1548
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLunin, V.V. / Evdokimova, E. / Kudritskaya, M. / Cuff, M.E. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of hypothetical protein AF1548 from Archaeoglobus fulgidus
Authors: Lunin, V.V. / Evdokimova, E. / Kudritskaya, M. / Cuff, M.E. / Joachimiak, A. / Edwards, A. / Savchenko, A.
History
DepositionDec 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 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_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_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

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Assembly

Deposited unit
A: Hypothetical protein AF1548
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,50611
Polymers22,6061
Non-polymers90010
Water2,720151
1
A: Hypothetical protein AF1548
hetero molecules

A: Hypothetical protein AF1548
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,01222
Polymers45,2122
Non-polymers1,80020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4600 Å2
ΔGint-224 kcal/mol
Surface area18410 Å2
MethodPISA
2
A: Hypothetical protein AF1548
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)141,03566
Polymers135,6356
Non-polymers5,40060
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area20330 Å2
ΔGint-773 kcal/mol
Surface area49800 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)124.225, 124.225, 62.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

21A-427-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: Y, X, -Z

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Components

#1: Protein Hypothetical protein AF1548


Mass: 22605.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: modified pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O28724
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.5 Å3/Da / Density % sol: 65 %
Description: The original data collected includes freidel pairs thus the number of reflection reported in the data collection is almost twice that used in the refinement
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M (NH4)2SO4, 15% PEG 3350, 2% PEG 400, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 46454 / Num. obs: 46443 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.85→1.92 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.378 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1266 5.1 %RANDOM
Rwork0.20163 ---
obs0.20321 23669 99.93 %-
all-23669 --
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: 24.582 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.61 Å20 Å2
2--1.21 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 46 151 1666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221552
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9932098
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.0195187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.88423.94471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39815283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.831510
X-RAY DIFFRACTIONr_chiral_restr0.1160.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021134
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.2700
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21051
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2140
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0241.5946
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65721474
X-RAY DIFFRACTIONr_scbond_it2.6073689
X-RAY DIFFRACTIONr_scangle_it3.9634.5622
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 78 -
Rwork0.231 1729 -
obs--99.83 %

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