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- PDB-3i3f: Hypothetical protein from Giardia lamblia GL50803_14299 -

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Basic information

Entry
Database: PDB / ID: 3i3f
TitleHypothetical protein from Giardia lamblia GL50803_14299
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / hypothetical / structural genomics / NIAID / deCODE / infectious disease / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


: / deaminase activity / mitochondrion / cytosol
Similarity search - Function
RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
butanoic acid / PENTANOIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Hypothetical protein from Giardia lamblia GL50803_14299
Authors: Arakaki, T.L. / Abendroth, J. / Staker, B.L.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification / _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: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9966
Polymers46,7043
Non-polymers2923
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-15 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.900, 119.900, 104.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-262-

HOH

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Components

#1: Protein Hypothetical protein


Mass: 15567.940 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / Gene: GL50803_14299 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8BD71
#2: Chemical ChemComp-LEA / PENTANOIC ACID / VALERIC ACID


Mass: 102.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O2
#3: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsAUTHOR STATE THA THESE GROUPS WERE MODELED IN RESIDUAL ELECTRON DENSITY BASED UPON THE BEST BIT, ...AUTHOR STATE THA THESE GROUPS WERE MODELED IN RESIDUAL ELECTRON DENSITY BASED UPON THE BEST BIT, BUT THE EXACT IDENTITY OF THE LIGANDS MAY NOT BE CORRECT.

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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: 2.17 Å3/Da / Density % sol: 38.87 %
Crystal growTemperature: 290 K / Method: sitting drop, vapor diffusion / pH: 5.5
Details: 100 mM Tris, pH 5.5, 25% PEG 3350, 200 mM ammonium acetate, sitting drop, vapor diffusion, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: ADSC Quantum-315R CCD / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→39.41 Å / Num. all: 82643 / Num. obs: 82643 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.424.80.5221.455749116010.52296.6
1.42-1.516.50.367273335113580.367100
1.51-1.616.50.2383.169392106970.238100
1.61-1.746.50.1654.56513899840.165100
1.74-1.916.50.1225.16037492180.122100
1.91-2.136.60.08675465583400.086100
2.13-2.466.60.0827.34865274030.082100
2.46-3.026.60.05910.14152963150.059100
3.02-4.276.50.04812.13210749280.048100
4.27-39.416.20.02722.11726627990.02798.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.54 Å39.41 Å
Translation1.54 Å39.41 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→37.35 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.89 / SU B: 0.872 / SU ML: 0.036 / SU R Cruickshank DPI: 0.056 / SU Rfree: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4134 5 %RANDOM
Rwork0.176 ---
obs0.177 82626 100 %-
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 max: 56.86 Å2 / Biso mean: 14.501 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.35→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 20 443 3434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0223127
X-RAY DIFFRACTIONr_bond_other_d0.0010.022080
X-RAY DIFFRACTIONr_angle_refined_deg0.8931.9744265
X-RAY DIFFRACTIONr_angle_other_deg0.72635103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3315416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.1524.452146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.79615529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6251524
X-RAY DIFFRACTIONr_chiral_restr0.0520.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
X-RAY DIFFRACTIONr_mcbond_it0.3181.51968
X-RAY DIFFRACTIONr_mcbond_other0.0431.5802
X-RAY DIFFRACTIONr_mcangle_it0.59923211
X-RAY DIFFRACTIONr_scbond_it0.72431159
X-RAY DIFFRACTIONr_scangle_it1.2244.51038
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 260 -
Rwork0.255 5432 -
all-5692 -
obs--100 %

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