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- PDB-1hzd: CRYSTAL STRUCTURE OF HUMAN AUH PROTEIN, AN RNA-BINDING HOMOLOGUE ... -

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Basic information

Entry
Database: PDB / ID: 1hzd
TitleCRYSTAL STRUCTURE OF HUMAN AUH PROTEIN, AN RNA-BINDING HOMOLOGUE OF ENOYL-COA HYDRATASE
ComponentsAU-BINDING PROTEIN/ENOYL-COA HYDRATASE
KeywordsLYASE / RNA-binding protein / enoyl-CoA hydratase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


methylglutaconyl-CoA hydratase / itaconyl-CoA hydratase / methylglutaconyl-CoA hydratase activity / itaconyl-CoA hydratase activity / 3-methylglutaconic aciduria / L-leucine catabolic process / enoyl-CoA hydratase activity / Branched-chain amino acid catabolism / fatty acid beta-oxidation / mRNA 3'-UTR binding ...methylglutaconyl-CoA hydratase / itaconyl-CoA hydratase / methylglutaconyl-CoA hydratase activity / itaconyl-CoA hydratase activity / 3-methylglutaconic aciduria / L-leucine catabolic process / enoyl-CoA hydratase activity / Branched-chain amino acid catabolism / fatty acid beta-oxidation / mRNA 3'-UTR binding / mitochondrial matrix / mitochondrion
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Methylglutaconyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKurimoto, K. / Fukai, S. / Nureki, O. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2001
Title: Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase.
Authors: Kurimoto, K. / Fukai, S. / Nureki, O. / Muto, Y. / Yokoyama, S.
History
DepositionJan 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AU-BINDING PROTEIN/ENOYL-COA HYDRATASE
B: AU-BINDING PROTEIN/ENOYL-COA HYDRATASE
C: AU-BINDING PROTEIN/ENOYL-COA HYDRATASE
D: AU-BINDING PROTEIN/ENOYL-COA HYDRATASE
E: AU-BINDING PROTEIN/ENOYL-COA HYDRATASE
F: AU-BINDING PROTEIN/ENOYL-COA HYDRATASE


Theoretical massNumber of molelcules
Total (without water)175,4296
Polymers175,4296
Non-polymers00
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23950 Å2
ΔGint-186 kcal/mol
Surface area59180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.13, 132.07, 80.04
Angle α, β, γ (deg.)90.0, 108.14, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AU-BINDING PROTEIN/ENOYL-COA HYDRATASE / AUH


Mass: 29238.154 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AUH / Plasmid: PGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13825, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.26 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, calcium acetate, sodium acetate, imidazole, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMsodium cacodylate1droppH6.5
29 %PEG80001drop
3100 mMcalcium acetate1drop
4100 mMsodium acetate1drop
510 mMimidazole1drop
6100 mMsodium cacodylate1reservoirpH6.5
718 %PEG80001reservoir
8200 mMcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 1999
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 76595 / Num. obs: 76595 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 16.994 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 2.673 / Num. unique all: 3601 / Rsym value: 0.125 / % possible all: 91.5
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. measured all: 236961
Reflection shell
*PLUS
Rmerge(I) obs: 0.123

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DUB

1dub


Resolution: 2.2→20 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh&Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 7679 10 %random
Rwork0.207 ---
all0.212 76592 --
obs0.212 68913 96.5 %-
Displacement parametersBiso mean: 36.4512 Å2
Baniso -1Baniso -2Baniso -3
1--5.755 Å20 Å2-1.677 Å2
2--6.47 Å20 Å2
3----0.715 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11973 0 0 309 12282
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.18733
X-RAY DIFFRACTIONc_dihedral_angle_d21.302
X-RAY DIFFRACTIONc_improper_angle_d0.81863
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2875 755 10 %
Rwork0.2268 6511 -
obs--91.95 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.302
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81863
LS refinement shell
*PLUS
% reflection Rfree: 10 %

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