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- PDB-6sbi: X-ray structure of murine Fumarylacetoacetate hydrolase domain co... -

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Basic information

Entry
Database: PDB / ID: 6sbi
TitleX-ray structure of murine Fumarylacetoacetate hydrolase domain containing protein 1 (FAHD1) in complex with inhibitor oxalate
ComponentsAcylpyruvase FAHD1, mitochondrial
KeywordsHYDROLASE / Oxalate binding / TCA cycle / mitochondria
Function / homology
Function and homology information


acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / Citric acid cycle (TCA cycle) / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / mitochondrial inner membrane / mitochondrion / nucleoplasm ...acylpyruvate hydrolase / fumarylpyruvate hydrolase activity / acylpyruvate hydrolase activity / Citric acid cycle (TCA cycle) / acetylpyruvate hydrolase activity / oxaloacetate decarboxylase / oxaloacetate decarboxylase activity / mitochondrial inner membrane / 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 family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / OXALATE ION / Acylpyruvase FAHD1, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRupp, B. / Naschberger, A. / Weiss, A.K.H.
Funding support Austria, 2items
OrganizationGrant numberCountry
European Commission512020 Austria
Austrian Science FundP28395-B26 Austria
CitationJournal: Biosci.Rep. / Year: 2020
Title: Structural and functional comparison of fumarylacetoacetate domain containing protein 1 in human and mouse.
Authors: Weiss, A.K.H. / Naschberger, A. / Cappuccio, E. / Metzger, C. / Mottes, L. / Holzknecht, M. / von Velsen, J. / Bowler, M.W. / Rupp, B. / Jansen-Durr, P.
History
DepositionJul 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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_initial_refinement_model / 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
C: Acylpyruvase FAHD1, mitochondrial
D: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,49923
Polymers117,6524
Non-polymers84719
Water59433
1
A: Acylpyruvase FAHD1, mitochondrial
B: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,26712
Polymers58,8262
Non-polymers44110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-94 kcal/mol
Surface area16350 Å2
MethodPISA
2
C: Acylpyruvase FAHD1, mitochondrial
D: Acylpyruvase FAHD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,23211
Polymers58,8262
Non-polymers4069
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-78 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.603, 103.348, 86.597
Angle α, β, γ (deg.)90.000, 90.210, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRSERSERAA10 - 22548 - 263
21THRTHRSERSERBB10 - 22548 - 263
12PROPROARGARGAA12 - 22450 - 262
22PROPROARGARGCC12 - 22450 - 262
13THRTHRSERSERAA10 - 22548 - 263
23THRTHRSERSERDD10 - 22548 - 263
14PROPROARGARGBB12 - 22450 - 262
24PROPROARGARGCC12 - 22450 - 262
15THRTHRSERSERBB10 - 22548 - 263
25THRTHRSERSERDD10 - 22548 - 263
16PROPROARGARGCC12 - 22450 - 262
26PROPROARGARGDD12 - 22450 - 262

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 29412.994 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fahd1, MNCb-4134 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8R0F8, acylpyruvate hydrolase, oxaloacetate decarboxylase

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Non-polymers , 5 types, 52 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 20% PEG 4000, 0.05M MgCl2, 0.1M MES pH5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 20, 2018
RadiationMonochromator: Diamond C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.7→44.38 Å / Num. obs: 15791 / % possible obs: 91.2 % / Redundancy: 3.43 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.108 / Rrim(I) all: 0.203 / Net I/σ(I): 4.2
Reflection shellResolution: 2.71→2.97 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 790 / CC1/2: 0.757 / Rpim(I) all: 0.351 / Rrim(I) all: 0.648 / % possible all: 51.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FOH

6foh


Resolution: 2.7→44.37 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.878 / SU B: 39.706 / SU ML: 0.372 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.505 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 756 4.8 %RANDOM
Rwork0.1869 ---
obs0.1893 15119 62.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.64 Å2 / Biso mean: 31.973 Å2 / Biso min: 1.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å20.24 Å2
2---1.66 Å20 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 2.7→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6704 0 39 33 6776
Biso mean--38.01 13.9 -
Num. residues----862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136910
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176647
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6459328
X-RAY DIFFRACTIONr_angle_other_deg1.1821.57515468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2115860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.40521.6300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.511151235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7741540
X-RAY DIFFRACTIONr_chiral_restr0.060.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021361
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A67150.08
12B67150.08
21A67210.07
22C67210.07
31A67590.08
32D67590.08
41B66400.08
42C66400.08
51B67640.07
52D67640.07
61C66770.09
62D66770.09
LS refinement shellResolution: 2.704→2.774 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.508 3 -
Rwork0.29 38 -
all-41 -
obs--2.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5123-0.238-0.28670.12370.12550.90830.0360.0505-0.0891-0.01730.00780.0343-0.15540.0563-0.04370.0274-0.01690.01210.0921-0.0390.032217.2998-1.318331.3929
20.40910.18330.09460.25510.32070.6112-0.0258-0.0444-0.0201-0.0524-0.0252-0.0057-0.1043-0.12350.0510.01880.0282-0.01110.0821-0.0350.01890.00683.615751.4422
30.61420.181-0.01490.2573-0.49141.16780.0137-0.05330.0551-0.0456-0.05240.00220.12130.10550.03880.02010.01880.0030.05550.01750.022434.755-23.78168.1903
40.5228-0.42330.27140.3616-0.27560.68170.05020.02670.0464-0.05930.0164-0.02420.1445-0.0611-0.06660.0337-0.0283-0.01720.08360.02440.020517.4321-18.7053-11.8368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 225
2X-RAY DIFFRACTION2B10 - 225
3X-RAY DIFFRACTION3C12 - 225
4X-RAY DIFFRACTION4D10 - 225

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