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- PDB-1qco: CRYSTAL STRUCTURE OF FUMARYLACETOACETATE HYDROLASE COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1qco
TitleCRYSTAL STRUCTURE OF FUMARYLACETOACETATE HYDROLASE COMPLEXED WITH FUMARATE AND ACETOACETATE
ComponentsFUMARYLACETOACETATE HYDROLASE
KeywordsHYDROLASE / MIXED BETA SANDWICH ROLL
Function / homology
Function and homology information


homogentisate catabolic process / fumarylacetoacetase / fumarylacetoacetase activity / Tyrosine catabolism / tyrosine catabolic process / L-phenylalanine catabolic process / arginine catabolic process / lipid metabolic process / metal ion binding
Similarity search - Function
Fumarylacetoacetase, N-terminal domain / Fumarylacetoacetase / Fumarylacetoacetase, N-terminal / Fumarylacetoacetase, N-terminal domain superfamily / Fumarylacetoacetase N-terminal / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family ...Fumarylacetoacetase, N-terminal domain / Fumarylacetoacetase / Fumarylacetoacetase, N-terminal / Fumarylacetoacetase, N-terminal domain superfamily / Fumarylacetoacetase N-terminal / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETOACETIC ACID / FUMARIC ACID / NICKEL (II) ION / Fumarylacetoacetase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsTimm, D.E. / Mueller, H.A. / Bhanumoorthy, P. / Harp, J.M. / Bunick, G.J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure and mechanism of a carbon-carbon bond hydrolase.
Authors: Timm, D.E. / Mueller, H.A. / Bhanumoorthy, P. / Harp, J.M. / Bunick, G.J.
History
DepositionMay 17, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUMARYLACETOACETATE HYDROLASE
B: FUMARYLACETOACETATE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,69213
Polymers92,8822
Non-polymers81011
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-80 kcal/mol
Surface area30630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.640, 110.940, 67.810
Angle α, β, γ (deg.)90.00, 102.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FUMARYLACETOACETATE HYDROLASE / / FAH


Mass: 46440.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: P35505, fumarylacetoacetase

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Non-polymers , 5 types, 540 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#5: Chemical ChemComp-AAE / ACETOACETIC ACID / Acetoacetic acid


Mass: 102.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, SODIUM CACODYLATE, NICKEL ACETATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
225 mMTris-HCl1drop
325 mM1dropCaCl2
417 %PEG80001reservoir
560 mMnickel acetate1reservoir
6180 mMsodium acetate1reservoir
7100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→27.9 Å / Num. obs: 67124 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.264 / % possible all: 60.9
Reflection
*PLUS
Num. measured all: 148826
Reflection shell
*PLUS
% possible obs: 60.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→27.9 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.192 3399 -RANDOM
Rwork0.159 ---
obs0.159 67102 91.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6457 0 37 529 7023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg24.31
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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