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- PDB-2c2n: Structure of human mitochondrial malonyltransferase -

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Basic information

Entry
Database: PDB / ID: 2c2n
TitleStructure of human mitochondrial malonyltransferase
ComponentsMALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE
KeywordsTRANSFERASE / FATTY ACID SYNTHASE / LIPID SYNTHESIS / MITOCHONDRION TRANSFERASE
Function / homology
Function and homology information


Mitochondrial Fatty Acid Beta-Oxidation / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid beta-oxidation / fatty acid biosynthetic process / mitochondrial matrix / mitochondrion / RNA binding
Similarity search - Function
Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alpha-Beta Plaits ...Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-(2-ETHOXYETHOXY)ETHANOL / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL / 1,2-DIMETHOXYETHANE / Malonyl-CoA-acyl carrier protein transacylase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWu, X. / Bunkoczi, G. / Smee, C. / Arrowsmith, C. / Sundstrom, M. / Weigelt, J. / Edwards, A. / von Delft, F. / Oppermann, U.
CitationJournal: Chem.Biol. / Year: 2009
Title: Structural Basis for Different Specificities of Acyltransferases Associated with the Human Cytosolic and Mitochondrial Fatty Acid Synthases.
Authors: Bunkoczi, G. / Misquitta, S. / Wu, X. / Lee, W.H. / Rojkova, A. / Kochan, G. / Kavanagh, K.L. / Oppermann, U. / Smith, S.
History
DepositionSep 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jan 29, 2014Group: Database references / Derived calculations
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE
B: MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,60314
Polymers75,3092
Non-polymers1,29512
Water10,359575
1
A: MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5879
Polymers37,6541
Non-polymers9338
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0165
Polymers37,6541
Non-polymers3624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.573, 84.828, 74.565
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A20 - 339
2115B20 - 339

NCS oper: (Code: given
Matrix: (-0.99969, 0.02342, 0.00849), (-0.02331, -0.99965, 0.01225), (0.00877, 0.01205, 0.99989)
Vector: 73.70608, 5.30501, 27.37836)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MALONYL COA-ACYL CARRIER PROTEIN TRANSACYLASE / MITOCHRODRIAL MALONYLTRANSFERASE / MCT


Mass: 37654.367 Da / Num. of mol.: 2 / Fragment: RESIDUES 60-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IVS2

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Non-polymers , 6 types, 587 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AE4 / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#4: Chemical ChemComp-DXE / 1,2-DIMETHOXYETHANE


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsINVOLVED IN THE TRANSFER OF A MALONYL MOIETY FROM MALONYL- COA TO THE FREE THIOL GROUP OF THE ...INVOLVED IN THE TRANSFER OF A MALONYL MOIETY FROM MALONYL- COA TO THE FREE THIOL GROUP OF THE MITOCHONDRIAL ACP PROTEIN.

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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: 2.2 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 32%PEG4000, 0.25M LI2SO4, 100MM TRIS-HCL, PH8.5, SITTING DROP, 293 K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0038
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0038 Å / Relative weight: 1
ReflectionResolution: 1.55→52 Å / Num. obs: 94082 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 2.44 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.28 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MLA

1mla


Resolution: 1.55→74.33 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.914 / SU ML: 0.07 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 20-22 CHAIN A WERE NOT VISIBLE IN THE DENSITY AND WERE NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2005 2.1 %RANDOM
Rwork0.178 ---
obs0.179 92079 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-1.66 Å2
2---0.65 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.55→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4779 0 74 575 5428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9656795
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1775634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23122.905210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79115806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9011535
X-RAY DIFFRACTIONr_chiral_restr0.110.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023778
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22634
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23445
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2540
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0841.53209
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59125037
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.73431986
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2084.51754
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1216medium positional0.190.5
1064loose positional0.545
1216medium thermal1.832
1064loose thermal2.410
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.302 130
Rwork0.285 6465
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)
11.0365-0.24850.27211.0937-0.22611.1010.0246-0.031-0.0154-0.0333-0.02990.0735-0.03620.04330.0053-0.094-0.0135-0.0203-0.12810.0118-0.048247.966415.612840.3069
21.56080.21840.69331.0411-0.36442.31620.1826-0.3986-0.04080.1583-0.0612-0.07460.2094-0.2346-0.1214-0.0563-0.0321-0.0011-0.0059-0.0083-0.081127.2429-10.823667.8229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 339
2X-RAY DIFFRACTION2B20 - 339

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