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- PDB-6foh: X-ray structure of homo sapiens Fumarylacetoacetate hydrolase dom... -

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Basic information

Entry
Database: PDB / ID: 6foh
TitleX-ray structure of homo sapiens Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) at 1.56A resolution.
ComponentsAcylpyruvase FAHD1, mitochondrial
KeywordsHYDROLASE/LYASE / FAHD 1 / Fumarylacetoacetate hydrolase domain containing protein 1 / HYDROLASE-LYASE complex
Function / homology
Function and homology information


acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / oxaloacetate tautomerase / oxaloacetate tautomerase activity / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / oxaloacetate metabolic process / Pyruvate metabolism ...acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / oxaloacetate tautomerase / oxaloacetate tautomerase activity / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / oxaloacetate metabolic process / Pyruvate metabolism / pyruvate metabolic process / mitochondrial matrix / mitochondrion / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase C-terminal / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Oxaloacetate tautomerase FAHD1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.56 Å
AuthorsNaschberger, A. / Weiss, A.K.H.
Funding support Austria, 3items
OrganizationGrant numberCountry
European integrated FP6-LIFESCIHEALTH project MiMAGE512020
Austria Wirtschaftsservice Gesellschaft (AWS) Austria
Austrian Science FundP28975 Austria
CitationJournal: Biochem. J. / Year: 2018
Title: Structural basis for the bi-functionality of human oxaloacetate decarboxylase FAHD1.
Authors: Weiss, A.K.H. / Naschberger, A. / Loeffler, J.R. / Gstach, H. / Bowler, M.W. / Holzknecht, M. / Cappuccio, E. / Pittl, A. / Etemad, S. / Dunzendorfer-Matt, T. / Scheffzek, K. / Liedl, K.R. / Jansen-Durr, P.
History
DepositionFeb 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.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.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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylpyruvase FAHD1, mitochondrial
B: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8586
Polymers49,7502
Non-polymers1084
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-62 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.090, 77.820, 119.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 8 - 224 / Label seq-ID: 8 - 224

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Acylpyruvase FAHD1, mitochondrial / Fumarylacetoacetate hydrolase domain-containing protein 1 / FAH domain-containing protein 1 / ...Fumarylacetoacetate hydrolase domain-containing protein 1 / FAH domain-containing protein 1 / Oxaloacetate decarboxylase / OAA decarboxylase / YisK-like protein


Mass: 24874.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAHD1, C16orf36, YISKL / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P587, acylpyruvate hydrolase, oxaloacetate decarboxylase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10% PEG4000 50mM MgCl2 100mM HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.56→65.29 Å / Num. obs: 58013 / % possible obs: 97.9 % / Redundancy: 4.77 % / CC1/2: 0.999 / Rrim(I) all: 0.071 / Net I/σ(I): 13.36
Reflection shellResolution: 1.56→1.6 Å / CC1/2: 0.518 / Rrim(I) all: 0.83

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.56→65.29 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.659 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18917 2794 4.8 %RANDOM
Rwork0.16202 ---
obs0.16335 55219 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0 Å2
2--0.12 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.56→65.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 4 306 3659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193550
X-RAY DIFFRACTIONr_bond_other_d0.0020.023394
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9094831
X-RAY DIFFRACTIONr_angle_other_deg0.95237915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25223.704135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62515632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0481519
X-RAY DIFFRACTIONr_chiral_restr0.0930.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213918
X-RAY DIFFRACTIONr_gen_planes_other0.0020.019685
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2534.2151776
X-RAY DIFFRACTIONr_mcbond_other3.2524.2091775
X-RAY DIFFRACTIONr_mcangle_it4.6887.8492234
X-RAY DIFFRACTIONr_mcangle_other4.6877.8582235
X-RAY DIFFRACTIONr_scbond_it5.0635.2261774
X-RAY DIFFRACTIONr_scbond_other5.0615.2291775
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3219.2452596
X-RAY DIFFRACTIONr_long_range_B_refined8.9629.43998
X-RAY DIFFRACTIONr_long_range_B_other8.93128.9763925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13722 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.563→1.604 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 188 -
Rwork0.278 3920 -
obs--95.51 %

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