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- PDB-2hzy: Mouse fumarylacetoacetate hydrolase complexes with a transition-s... -

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Basic information

Entry
Database: PDB / ID: 2hzy
TitleMouse fumarylacetoacetate hydrolase complexes with a transition-state mimic of the complete substrate
ComponentsFumarylacetoacetase
KeywordsHYDROLASE / transition-state mimicking complex
Function / homology
Function and homology information


fumarylacetoacetase / fumarylacetoacetase activity / homogentisate catabolic process / 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
Chem-DHJ / : / NICKEL (II) ION / Fumarylacetoacetase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHurley, T.D. / Timm, D.E.
CitationJournal: Biochem.J. / Year: 2007
Title: Slow-onset inhibition of fumarylacetoacetate hydrolase by phosphinate mimics of the tetrahedral intermediate: kinetics, crystal structure and pharmacokinetics.
Authors: Bateman, R.L. / Ashworth, J. / Witte, J.F. / Baker, L.J. / Bhanumoorthy, P. / Timm, D.E. / Hurley, T.D. / Grompe, M. / McClard, R.W.
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_alt_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_asym_id / _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_alt_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.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fumarylacetoacetase
B: Fumarylacetoacetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,85219
Polymers92,5932
Non-polymers1,25917
Water17,943996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-126 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.144, 109.472, 67.491
Angle α, β, γ (deg.)90.00, 102.35, 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 Fumarylacetoacetase / Fumarylacetoacetate hydrolase / Beta-diketonase / FAA


Mass: 46296.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fah / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P35505, fumarylacetoacetase

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Non-polymers , 6 types, 1013 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-DHJ / 4-(2-CARBOXYETHYL)(HYDROXY)PHOSPHORYL]-3-OXOBUTANOIC ACID / 4-[(2-CARBOXYETHYL)HYDROXYPHOSPHINYL] 3-OXOBUTYRIC ACID


Mass: 238.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11O7P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 996 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium cacodylate, 0.3 M Sodium acetate, 30% (w/v) PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: APS-1 / Detector: CCD / Date: Dec 1, 2001 / Details: ID-19
RadiationMonochromator: 19-ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 188128 / % possible obs: 94.6 % / Observed criterion σ(F): 0.2 / Redundancy: 4.37 % / Biso Wilson estimate: 17.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.444 / % possible all: 79.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QCN

1qcn


Resolution: 1.35→24.14 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.92 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18815 9466 5 %RANDOM
Rwork0.16799 ---
all0.16901 188088 --
obs0.16901 188088 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.23 Å2
2--1.41 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.35→24.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6489 0 45 998 7532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0216695
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.959086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8035831
X-RAY DIFFRACTIONr_chiral_restr0.120.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025163
X-RAY DIFFRACTIONr_nbd_refined0.2130.23147
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2736
X-RAY DIFFRACTIONr_metal_ion_refined0.3410.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.238
X-RAY DIFFRACTIONr_mcbond_it1.0571.54156
X-RAY DIFFRACTIONr_mcangle_it1.81926711
X-RAY DIFFRACTIONr_scbond_it2.63532539
X-RAY DIFFRACTIONr_scangle_it4.0554.52375
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 557
Rwork0.281 10397

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