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- PDB-1khi: CRYSTAL STRUCTURE OF HEX1 -

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Basic information

Entry
Database: PDB / ID: 1khi
TitleCRYSTAL STRUCTURE OF HEX1
ComponentsHex1
KeywordsSTRUCTURAL PROTEIN / HEX1 / NEUROSPORA CRASSA / MEMBRANE SEALING / PEROXISOMAL TARGET
Function / homology
Function and homology information


Woronin body / positive regulation of translational termination / positive regulation of translational elongation / cell septum / translational elongation / translation elongation factor activity / ribosome binding / RNA binding
Similarity search - Function
Hex1, S1 domain / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / SH3 type barrels. - #30 / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Hex1, S1 domain / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / SH3 type barrels. - #30 / Nucleic acid-binding proteins / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Woronin body major protein
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.78 Å
AuthorsYuan, P. / Swaminathan, K.
Citation
Journal: NAT.STRUCT.BIOL. / Year: 2003
Title: A HEX-1 crystal lattice required for Woronin body function in Neurospora crassa
Authors: Yuan, P. / Jedd, G. / Kumaran, D. / Swaminathan, S. / Shio, H. / Hewitt, D. / Chua, N.-H. / Swaminathan, K.
#1: Journal: NAT.CELL BIOL. / Year: 2000
Title: A new self-assembled peroxisomal vesicle required for efficient resealing of the plasma membrane
Authors: Jedd, G. / Chua, N.-H.
History
DepositionNov 30, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 22, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hex1


Theoretical massNumber of molelcules
Total (without water)19,1511
Polymers19,1511
Non-polymers00
Water2,360131
1
A: Hex1

A: Hex1


Theoretical massNumber of molelcules
Total (without water)38,3012
Polymers38,3012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area2420 Å2
ΔGint-8 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.427, 57.427, 196.975
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Hex1 / Woronin body major protein


Mass: 19150.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Plasmid: PGEX61 / Gene (production host): HEX1 (1-176) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)LYS-S / References: UniProt: P87252
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.35 Å3/Da / Density % sol: 47.24 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mg/mlprotein1drop
260 mMTris1reservoirpH7.5
3210 mM1reservoirNaCl
430 mM1reservoirCaCl2
55 %(w/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.978797, 0.978441, 0.930
DetectorType: BRANDEIS / Detector: CCD / Date: Apr 13, 2001
RadiationMonochromator: DIAMOND / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9787971
20.9784411
30.931
ReflectionResolution: 1.78→99 Å / Num. obs: 16231 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.055 / Net I/σ(I): -3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.159 / Rsym value: 0.146 / % possible all: 85.1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 18047 / Num. measured all: 123270 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.78→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 220231.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1340 9.9 %RANDOM
Rwork0.198 ---
obs0.198 13538 73 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.8285 Å2 / ksol: 0.532008 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å21.13 Å20 Å2
2---0.92 Å20 Å2
3---1.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å-0.03 Å
Refinement stepCycle: LAST / Resolution: 1.78→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 0 131 1259
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4771.5
X-RAY DIFFRACTIONc_mcangle_it2.4072
X-RAY DIFFRACTIONc_scbond_it2.1832
X-RAY DIFFRACTIONc_scangle_it3.2472.5
LS refinement shellResolution: 1.78→1.89 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.208 82 9.3 %
Rwork0.163 798 -
obs--28.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 13542 / σ(F): 3 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.351
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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