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- PDB-3b7w: Crystal structure of human acyl-CoA synthetase medium-chain famil... -

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Basic information

Entry
Database: PDB / ID: 3b7w
TitleCrystal structure of human acyl-CoA synthetase medium-chain family member 2A, with L64P mutation
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 / 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
Acyl-coenzyme A synthetase ACSM2A, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPilka, E.S. / Kochan, G.T. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / 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
DepositionOct 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)63,5937
Polymers63,3351
Non-polymers2586
Water8,251458
1
A: Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)190,77821
Polymers190,0043
Non-polymers77518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)98.426, 109.173, 176.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 1.4M Na citrate, 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: Sep 25, 2007 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50.57 Å / Num. all: 63810 / Num. obs: 60580 / % possible obs: 98.9 % / Observed criterion σ(I): 2.06 / Redundancy: 4.6 % / Rmerge(I) obs: 0.077 / Rsym value: 0.04 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2 / Rsym value: 0.446 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PG3

1pg3


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.004 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21385 3225 5.1 %RANDOM
Rwork0.16903 ---
obs0.17136 60580 98.81 %-
all-60580 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.86 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2--0.8 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 11 458 4595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224263
X-RAY DIFFRACTIONr_bond_other_d0.0010.022873
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9625804
X-RAY DIFFRACTIONr_angle_other_deg0.93937044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62424.32169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08915717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4091521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02825
X-RAY DIFFRACTIONr_nbd_refined0.1980.2793
X-RAY DIFFRACTIONr_nbd_other0.1950.23065
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22018
X-RAY DIFFRACTIONr_nbtor_other0.0880.22253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2362
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.82332922
X-RAY DIFFRACTIONr_mcbond_other1.15931091
X-RAY DIFFRACTIONr_mcangle_it4.59954346
X-RAY DIFFRACTIONr_scbond_it7.7271761
X-RAY DIFFRACTIONr_scangle_it9.204111452
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 237 -
Rwork0.242 4408 -
obs--97.81 %
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)
11.2267-0.0911-0.0070.6208-0.08460.1861-0.0171-0.1159-0.06490.04050.0064-0.05990.03420.00760.0108-0.04990.0150.0018-0.03580.0269-0.043615.526319.446253.1223
22.96670.23730.06440.70.54822.7466-0.03510.28320.2949-0.01890.0527-0.0586-0.40590.2854-0.0176-0.0232-0.08410.00290.04620.0461-0.2179.746835.72676.567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA33 - 46326 - 456
2X-RAY DIFFRACTION2AA464 - 569457 - 562

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