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- PDB-2wd9: CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMIL... -

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Basic information

Entry
Database: PDB / ID: 2wd9
TitleCRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A (L64P MUTATION) IN COMPLEX WITH IBUPROFEN
ComponentsACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
KeywordsLIGASE / NUCLEOTIDE-BINDING / FATTY ACID METABOLISM / TRANSIT PEPTIDE / LIPID METABOLISM / NUCLEOTIDE BINDING / MITOCHONDRION / METAL-BINDING / LIGASE ACTIVITY / MEDIUM-CHAIN FATTY ACID / FATTY ACID METABOLIC PROCESS / MAGNESIUM / ATP-BINDING
Function / homology
Function and homology information


Conjugation of salicylate with glycine / fatty acid ligase activity / decanoate-CoA ligase activity / medium-chain acyl-CoA ligase / : / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / acyl-CoA metabolic process / fatty-acyl-CoA synthase activity ...Conjugation of salicylate with glycine / fatty acid ligase activity / decanoate-CoA ligase activity / medium-chain acyl-CoA ligase / : / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / acyl-CoA metabolic process / fatty-acyl-CoA synthase activity / triglyceride homeostasis / Aspirin ADME / fatty acid biosynthetic process / glucose homeostasis / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
ANL, C-terminal domain / ANL, N-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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily ...ANL, C-terminal domain / ANL, N-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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IBUPROFEN / Acyl-coenzyme A synthetase ACSM2A, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYue, W.W. / Kochan, G.T. / Pilka, E.S. / Bhatia, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U.
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. / Delft, F.V. / Oppermann, U. / Yue, W.W.
History
DepositionMar 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
B: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
C: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,2878
Polymers189,6193
Non-polymers6675
Water3,873215
1
A: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4132
Polymers63,2061
Non-polymers2061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4373
Polymers63,2061
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4373
Polymers63,2061
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.320, 98.320, 381.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISTHRTHR3AA37 - 38530 - 378
21HISHISTHRTHR3BB37 - 38530 - 378
31HISHISTHRTHR3CC37 - 38530 - 378
12TYRTYRASNASN5AA390 - 467383 - 460
22TYRTYRASNASN5BB390 - 467383 - 460
32TYRTYRASNASN5CC390 - 467383 - 460
13SERSERLEULEU4AA468 - 550461 - 543
23SERSERLEULEU4BB468 - 550461 - 543
33SERSERLEULEU4CC468 - 550461 - 543

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Components

#1: Protein ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL / ACYL-COENZYME A SYNTHETASE ACSM2A / ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A / MIDDLE- ...ACYL-COENZYME A SYNTHETASE ACSM2A / ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A / MIDDLE-CHAIN ACYL-COA SYNTHETASE 2A / BUTYRYL COENZYME A SYNTHETASE 2A / BUTYRATE-COA LIGASE 2A


Mass: 63206.438 Da / Num. of mol.: 3 / Fragment: RESIDUES 32-576 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q08AH3, medium-chain acyl-CoA ligase
#2: Chemical ChemComp-IBP / IBUPROFEN / 2-(4-ISOBUTYLPHENYL)PROPIONIC ACID / Dexibuprofen


Mass: 206.281 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H18O2 / Comment: antiinflammatory, medication*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 64 TO PRO ENGINEERED RESIDUE IN CHAIN B, LEU 64 TO PRO ...ENGINEERED RESIDUE IN CHAIN A, LEU 64 TO PRO ENGINEERED RESIDUE IN CHAIN B, LEU 64 TO PRO ENGINEERED RESIDUE IN CHAIN C, LEU 64 TO PRO

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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: 2.43 Å3/Da / Density % sol: 49.39 % / Description: NONE
Crystal growDetails: 0.2M AM ACETATE, 0.1M TRIS PH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 11, 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: 2.6→38.92 Å / Num. obs: 54507 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 10.1
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B7W

3b7w


Resolution: 2.6→38.92 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.882 / SU B: 26.872 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.258 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2842 5 %RANDOM
Rwork0.235 ---
obs0.236 54057 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.62 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12363 0 47 215 12625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212811
X-RAY DIFFRACTIONr_bond_other_d0.0010.028665
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.96617429
X-RAY DIFFRACTIONr_angle_other_deg2.199321240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77251629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70724.325511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.186152181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0831564
X-RAY DIFFRACTIONr_chiral_restr0.0650.21953
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114185
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022479
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_it0.8071.58027
X-RAY DIFFRACTIONr_mcbond_other0.1081.53253
X-RAY DIFFRACTIONr_mcangle_it1.396212982
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.39534784
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5154.54435
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

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2024tight positional0.080.05
2B2024tight positional0.070.05
3C2024tight positional0.080.05
1A1531medium positional0.50.5
2B1531medium positional0.510.5
3C1531medium positional0.850.5
1A2938loose positional0.155
2B2938loose positional0.135
3C2938loose positional0.145
1A2024tight thermal0.380.5
2B2024tight thermal0.580.5
3C2024tight thermal0.620.5
1A1531medium thermal1.292
2B1531medium thermal1.472
3C1531medium thermal1.632
1A2938loose thermal0.5810
2B2938loose thermal0.710
3C2938loose thermal0.7410
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 186 -
Rwork0.335 3555 -
obs--87.59 %
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)
114.425410.72679.37517.98496.96586.10450.2122-0.2010.02950.2127-0.13670.09950.1061-0.2725-0.07550.62790.51140.25211.85610.6110.74345.7980.06113.683
21.01070.1434-0.22660.8753-0.34391.2686-0.0002-0.0751-0.06210.0006-0.0165-0.09960.10350.10310.01660.05740.0204-0.00940.05180.00480.015527.249.09122.65
37.8127-0.7494-2.85013.27070.91433.2290.14210.11230.76960.0348-0.0549-0.195-0.31070.0446-0.08730.10040.023-0.01880.06660.0240.103722.71134.02716.713
40.7594-0.21160.64430.1526-0.11321.2834-0.0063-0.01260.00060.06910.01380.0086-0.0395-0.0444-0.00750.09040.0080.00530.099-0.00090.00146.31621.15928.528
50.7788-1.0317-0.74022.50810.42642.0643-0.12320.00180.02980.09810.09580.162-0.2983-0.06120.02740.22460.008-0.080.11990.00250.059916.81428.71849.339
61.1644-0.09350.31030.9434-0.531.480.00260.06890.0481-0.058-0.0232-0.1027-0.080.16820.02060.0481-0.00190.01210.0628-0.0040.015641.866-22.965-6.886
78.4202-3.77998.92393.0504-2.153511.99490.2493-0.3354-0.52750.04110.37280.18580.4699-0.0543-0.62210.1046-0.022-0.02750.13590.04840.094127.287-23.592-6.643
81.89250.42520.69762.0751-0.7540.910.0689-0.0076-0.0034-0.02710.00870.34110.0879-0.1713-0.07760.11090.00350.01580.1318-0.04810.090319.004-26.576-11.171
90.12910.17750.01680.54890.3941.4830.0067-0.0525-0.0394-0.0919-0.0062-0.00470.0125-0.1047-0.00040.12450.0007-0.04170.09910.02410.029826.1-43.7741.466
101.57290.1982-0.70041.6213-0.25632.6218-0.0004-0.0441-0.12360.0841-0.06460.25890.0839-0.30070.0650.0648-0.01590.00550.1185-0.01130.059518.753-33.30820.289
1114.7495-5.1093-7.3391.86012.55533.65870.67990.27562.4337-0.03250.3242-0.7818-0.2581-0.1103-1.00412.1251-0.0642-0.32671.14420.1921.3451-6.5840.55840.302
121.08110.0877-0.39191.0723-0.13850.9655-0.0327-0.0744-0.10040.07930.0014-0.00290.10290.15580.03130.10110.01310.00390.1285-0.00710.027-11.123-26.96138.944
130.11650.1699-0.60116.39654.10698.5008-0.0983-0.0379-0.0559-0.1120.4303-0.00760.4188-0.0492-0.33190.6574-0.2138-0.06670.77760.03590.9937-38.247-34.83249.397
140.13-0.1303-0.18410.36030.24710.69560.0308-0.09860.01180.1422-0.00980.0577-0.1365-0.0017-0.0210.2249-0.03270.03390.2043-0.0220.1318-26.167-9.07135.831
152.94140.03711.31291.296-0.65752.82680.0852-0.23140.20610.2648-0.1050.3477-0.2429-0.24940.01980.0972-0.01110.05610.0923-0.04790.1184-33.661-19.56614.259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 43
2X-RAY DIFFRACTION2A44 - 322
3X-RAY DIFFRACTION3A323 - 360
4X-RAY DIFFRACTION4A361 - 502
5X-RAY DIFFRACTION5A503 - 569
6X-RAY DIFFRACTION6B37 - 256
7X-RAY DIFFRACTION7B257 - 265
8X-RAY DIFFRACTION8B266 - 389
9X-RAY DIFFRACTION9B390 - 503
10X-RAY DIFFRACTION10B504 - 569
11X-RAY DIFFRACTION11C34 - 39
12X-RAY DIFFRACTION12C40 - 321
13X-RAY DIFFRACTION13C322 - 329
14X-RAY DIFFRACTION14C330 - 496
15X-RAY DIFFRACTION15C497 - 569

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