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- PDB-1fl9: THE YJEE PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1fl9
TitleTHE YJEE PROTEIN
ComponentsHYPOTHETICAL PROTEIN HI0065
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / nucleotide-binding fold / Structure 2 Function Project / S2F
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine modification / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
tRNA threonylcarbamoyl adenosine modification protein TsaE / Threonylcarbamoyl adenosine biosynthesis protein TsaE / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / tRNA threonylcarbamoyladenosine biosynthesis protein TsaE
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsTeplyakov, A. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2002
Title: Crystal structure of the YjeE protein from Haemophilus influenzae: a putative Atpase involved in cell wall synthesis
Authors: Teplyakov, A. / Obmolova, G. / Tordova, M. / Thanki, N. / Bonander, N. / Eisenstein, E. / Howard, A.J. / Gilliland, G.L.
History
DepositionAug 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Feb 7, 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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_conn.ptnr2_label_seq_id / _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 HI0065
B: HYPOTHETICAL PROTEIN HI0065
C: HYPOTHETICAL PROTEIN HI0065
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4086
Polymers54,8063
Non-polymers6023
Water55831
1
A: HYPOTHETICAL PROTEIN HI0065
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4692
Polymers18,2691
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HYPOTHETICAL PROTEIN HI0065
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4692
Polymers18,2691
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HYPOTHETICAL PROTEIN HI0065
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4692
Polymers18,2691
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.400, 73.000, 96.800
Angle α, β, γ (deg.)90.00, 110.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HYPOTHETICAL PROTEIN HI0065


Mass: 18268.768 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: PLASMID T7-HIS TAG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P44492
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M Tris, 1.5% PEG400, 1.5M ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.6 Mammonium sulfate1reservoir
32 %(w/v)PEG4001reservoir
40.1 MTris-HCl1reservoirpH7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.01
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 132000 / Num. obs: 132000 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 21.5
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 8 % / Rmerge(I) obs: 0.158 / Num. unique all: 1000 / % possible all: 90
Reflection
*PLUS
Lowest resolution: 10 Å / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Rmerge(I) obs: 0.158

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→10 Å / σ(F): 3 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 820 -random
Rwork0.22 ---
all0.22 16442 --
obs0.22 15622 95 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 3 31 3799
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d2.1
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor obs: 0.22 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1

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