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- PDB-7lub: Crystal structure of recombinant human fumarase in complex with D... -

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Basic information

Entry
Database: PDB / ID: 7lub
TitleCrystal structure of recombinant human fumarase in complex with D-2-amino-3-phosphono-propionic acid
ComponentsFumarate hydratase, mitochondrialFumarase
KeywordsLYASE / Fumarase
Function / homology
Function and homology information


regulation of arginine metabolic process / tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / Citric acid cycle (TCA cycle) / malate metabolic process / urea cycle / positive regulation of double-strand break repair via nonhomologous end joining / homeostasis of number of cells within a tissue ...regulation of arginine metabolic process / tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / Citric acid cycle (TCA cycle) / malate metabolic process / urea cycle / positive regulation of double-strand break repair via nonhomologous end joining / homeostasis of number of cells within a tissue / tricarboxylic acid cycle / site of double-strand break / chromosome / positive regulation of cold-induced thermogenesis / histone binding / mitochondrial matrix / DNA repair / DNA damage response / mitochondrion / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
D-2-AMINO-3-PHOSPHONO-PROPIONIC ACID / Fumarate hydratase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCardoso, I.A. / Nonato, M.C.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/25075-0 Brazil
CitationJournal: Science / Year: 2023
Title: Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase.
Authors: Hicks, K.G. / Cluntun, A.A. / Schubert, H.L. / Hackett, S.R. / Berg, J.A. / Leonard, P.G. / Ajalla Aleixo, M.A. / Zhou, Y. / Bott, A.J. / Salvatore, S.R. / Chang, F. / Blevins, A. / Barta, P. ...Authors: Hicks, K.G. / Cluntun, A.A. / Schubert, H.L. / Hackett, S.R. / Berg, J.A. / Leonard, P.G. / Ajalla Aleixo, M.A. / Zhou, Y. / Bott, A.J. / Salvatore, S.R. / Chang, F. / Blevins, A. / Barta, P. / Tilley, S. / Leifer, A. / Guzman, A. / Arok, A. / Fogarty, S. / Winter, J.M. / Ahn, H.C. / Allen, K.N. / Block, S. / Cardoso, I.A. / Ding, J. / Dreveny, I. / Gasper, W.C. / Ho, Q. / Matsuura, A. / Palladino, M.J. / Prajapati, S. / Sun, P. / Tittmann, K. / Tolan, D.R. / Unterlass, J. / VanDemark, A.P. / Vander Heiden, M.G. / Webb, B.A. / Yun, C.H. / Zhao, P. / Wang, B. / Schopfer, F.J. / Hill, C.P. / Nonato, M.C. / Muller, F.L. / Cox, J.E. / Rutter, J.
History
DepositionFeb 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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: Fumarate hydratase, mitochondrial
B: Fumarate hydratase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8937
Polymers100,2792
Non-polymers6145
Water5,368298
1
A: Fumarate hydratase, mitochondrial
B: Fumarate hydratase, mitochondrial
hetero molecules

A: Fumarate hydratase, mitochondrial
B: Fumarate hydratase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,78614
Polymers200,5584
Non-polymers1,22910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area33800 Å2
ΔGint-201 kcal/mol
Surface area52330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.903, 190.903, 116.243
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-761-

HOH

21A-792-

HOH

31A-823-

HOH

41B-787-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 49 - 510 / Label seq-ID: 5 - 466

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

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Components

#1: Protein Fumarate hydratase, mitochondrial / Fumarase / Fumarase


Mass: 50139.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07954, fumarate hydratase
#2: Chemical ChemComp-APO / D-2-AMINO-3-PHOSPHONO-PROPIONIC ACID


Type: D-peptide linking / Mass: 169.073 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Hepes pH 7.5, 1% v/v 2-methylpentanediol and 16% m/v PEG 10 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRUS / Beamline: MANACA / Wavelength: 1.3236 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3236 Å / Relative weight: 1
ReflectionResolution: 2.15→49.85 Å / Num. obs: 67921 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 0.999 / Net I/σ(I): 15
Reflection shellResolution: 2.15→2.2 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4478 / CC1/2: 0.458 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UPP

5upp


Resolution: 2.15→49.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.159 / SU ML: 0.126 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 3399 5 %5%
Rwork0.1858 ---
obs0.1869 64478 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.22 Å2 / Biso mean: 47.766 Å2 / Biso min: 22.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.15→49.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6824 0 44 300 7168
Biso mean--54.55 51.16 -
Num. residues----922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0137009
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176701
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.6419514
X-RAY DIFFRACTIONr_angle_other_deg1.1741.57715406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48623.913299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.981151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3051526
X-RAY DIFFRACTIONr_chiral_restr0.0520.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021483
Refine LS restraints NCS

Ens-ID: 1 / Number: 14212 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 214 -
Rwork0.308 4722 -
all-4936 -
obs--100 %

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