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- PDB-3day: Crystal structure of human acyl-CoA synthetase medium-chain famil... -

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Basic information

Entry
Database: PDB / ID: 3day
TitleCrystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with AMP-CPP
ComponentsAcyl-coenzyme A synthetase ACSM2A, mitochondrial precursor
KeywordsLIGASE / MIDDLE-CHAIN ACYL-COA SYNTHETASE / XENOBIOTIC/MEDIUM-CHAIN FATTY ACID-COA LIGASE / STRUCTURAL GENOMICS CONSORTIUM / SGC / ATP-BINDING / FATTY ACID METABOLISM / LIPID METABOLISM / MAGNESIUM / METAL-BINDING / MITOCHONDRION / NUCLEOTIDE-BINDING POLYMORPHISM / TRANSIT PEPTIDE
Function / homology
Function and homology information


decanoate-CoA ligase activity / Conjugation of salicylate with glycine / medium-chain acyl-CoA ligase / fatty acid ligase activity / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / medium-chain fatty acid-CoA ligase activity / fatty-acyl-CoA synthase activity / acyl-CoA metabolic process ...decanoate-CoA ligase activity / Conjugation of salicylate with glycine / medium-chain acyl-CoA ligase / fatty acid ligase activity / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / medium-chain fatty acid-CoA ligase activity / fatty-acyl-CoA synthase activity / acyl-CoA metabolic process / triglyceride homeostasis / Aspirin ADME / fatty acid biosynthetic process / glucose homeostasis / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
: / ANL, N-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme ...: / ANL, N-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Acyl-coenzyme A synthetase ACSM2A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPilka, E.S. / Kochan, G.T. / Yue, W.W. / Bhatia, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wikstrom, M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A.
Authors: Kochan, G. / Pilka, E.S. / von Delft, F. / Oppermann, U. / Yue, W.W.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,20920
Polymers63,3351
Non-polymers87419
Water13,745763
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.508, 97.835, 120.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor / Acyl-CoA synthetase medium-chain family member 2A / Middle-chain acyl-CoA synthetase 2A / Butyrate- ...Acyl-CoA synthetase medium-chain family member 2A / Middle-chain acyl-CoA synthetase 2A / Butyrate-CoA ligase 2A / Butyryl coenzyme A synthetase 2A


Mass: 63334.562 Da / Num. of mol.: 1 / Fragment: Residues 32-577 / Mutation: L64P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACSM2A, ACSM2, MACS2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q08AH3, medium-chain acyl-CoA ligase

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Non-polymers , 7 types, 782 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 763 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.20M NaCl, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 17, 2008 / Details: OSMIC
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→32.72 Å / Num. all: 48550 / Num. obs: 45963 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Rsym value: 0.055 / Net I/σ(I): 11
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6604 / Rsym value: 0.303 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C5E

3c5e


Resolution: 1.95→31.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.675 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.143 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ADDITIONAL DENSITY IN THE ACTIVE SITE, PROBABLY UNIDENTIFIED ENDOGENOUS SUBSTRATE, WAS MODELLED AS A SET OF UNKNOWN (UNX) ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22033 2441 5 %RANDOM
Rwork0.16095 ---
all0.16398 45963 --
obs0.16398 45963 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.974 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.55 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 61 763 4974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224391
X-RAY DIFFRACTIONr_bond_other_d0.0010.022980
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.975986
X-RAY DIFFRACTIONr_angle_other_deg0.98937308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69524.426183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53215754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1911523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214849
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
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_it3.04832711
X-RAY DIFFRACTIONr_mcbond_other1.03131097
X-RAY DIFFRACTIONr_mcangle_it4.21654395
X-RAY DIFFRACTIONr_scbond_it6.74771680
X-RAY DIFFRACTIONr_scangle_it8.845111580
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 184 -
Rwork0.219 3127 -
obs--92.15 %
Refinement TLS params.Method: refined / Origin x: 23.9408 Å / Origin y: -9.3816 Å / Origin z: -17.9111 Å
111213212223313233
T-0.0389 Å20.0128 Å20.0105 Å2--0.036 Å20.0164 Å2---0.0331 Å2
L0.3795 °20.1067 °2-0.0029 °2-0.4883 °2-0.058 °2--0.2554 °2
S0.0049 Å °-0.0046 Å °-0.017 Å °0.005 Å °-0.0106 Å °-0.0366 Å °-0.0239 Å °-0.0041 Å °0.0057 Å °

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