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- PDB-1e20: The FMN binding protein AtHal3 -

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Basic information

Entry
Database: PDB / ID: 1.0E+20
TitleThe FMN binding protein AtHal3
ComponentsHALOTOLERANCE PROTEIN HAL3
KeywordsFLAVOPROTEIN / REGULATION / SIGNAL TRANSDUCTION / STRESS
Function / homology
Function and homology information


phosphopantothenoylcysteine decarboxylase / phosphopantothenoylcysteine decarboxylase activity / hyperosmotic salinity response / coenzyme A biosynthetic process
Similarity search - Function
Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / FLAVIN MONONUCLEOTIDE / NICKEL (II) ION / Phosphopantothenoylcysteine decarboxylase
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.02 Å
AuthorsAlbert, A. / Martinez-Ripoll, M. / Espinosa-Ruiz, A. / Yenush, L. / Culianez-Macia, F.A. / Serrano, R.
CitationJournal: Structure / Year: 2000
Title: The X-Ray Structure of the Fmn-Binding Protein Athal3 Provides the Structural Basis for the Activity of a Regulatory Subunit Involved in Signal Transduction
Authors: Albert, A. / Martinez-Ripoll, M. / Espinosa-Ruiz, A. / Yenush, L. / Culianez-Macia, F.A. / Serrano, R.
History
DepositionMay 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4May 30, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.5Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_sheet_hbond / pdbx_validate_close_contact ...pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_conf / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id ..._pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.sheet_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HALOTOLERANCE PROTEIN HAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9744
Polymers23,3811
Non-polymers5933
Water1,65792
1
A: HALOTOLERANCE PROTEIN HAL3
hetero molecules

A: HALOTOLERANCE PROTEIN HAL3
hetero molecules

A: HALOTOLERANCE PROTEIN HAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,92212
Polymers70,1433
Non-polymers1,7809
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)112.309, 112.309, 33.182
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-802-

NI

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Components

#1: Protein HALOTOLERANCE PROTEIN HAL3 / / HAL3


Mass: 23380.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9SWE5
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTER SER: RESIDUES FROM GLN A 203 - SER A 209 NOT SEEN IN THE ELECTRON DENSITY MAP MET: RESIDUES ...TER SER: RESIDUES FROM GLN A 203 - SER A 209 NOT SEEN IN THE ELECTRON DENSITY MAP MET: RESIDUES FROM MET A 1 - PRO A 17 NOT SEEN IN THE ELECTRON DENSITY MAP

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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

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 50 %
Crystal growpH: 7 / Details: 2.5 M AMMONIUM SULPHATE, PH 7.0
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MTris-HCl1drop
30.1 Mimidazole1drop
45 mMbeta-mercaptoethanol1drop
50.1 MTris-HCl1reservoir
62.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF NONIUS / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→36.76 Å / Num. obs: 15729 / % possible obs: 97.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 6
Reflection shellResolution: 2.02→2.12 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.8 / % possible all: 97.1
Reflection
*PLUS
Lowest resolution: 24.6 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 90.5 % / Rmerge(I) obs: 0.404

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.02→12 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES FROM LEU A 173 - GLY A 179 NOT SEEN IN ELECTRON DENSITY MAP, THEY HAVE BEEN MODELLED AND INCLUDED IN THIS ENTRY WITH ZERO OCCUPANCY
RfactorNum. reflection% reflectionSelection details
Rfree0.26 782 5 %RANDOM
Rwork0.21 ---
obs-14726 97 %-
Refinement stepCycle: LAST / Resolution: 2.02→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 36 92 1585
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21 / Rfactor Rfree: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / Rfactor Rfree: 0.244 / Rfactor obs: 0.256

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