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- PDB-2gce: The 1,1-proton transfer reaction mechanism by alpha-methylacyl-Co... -

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Basic information

Entry
Database: PDB / ID: 2gce
TitleThe 1,1-proton transfer reaction mechanism by alpha-methylacyl-CoA racemase is catalyzed by an aspartate/histidine pair and involves a smooth, methionine-rich surface for binding the fatty acyl moiety
Componentsprobable alpha-methylacyl-CoA racemase MCR
KeywordsISOMERASE / Alpha-methylacyl-CoA racemase / racemase / CoA transferase / proton transfer / Coenzyme A
Function / homology
Function and homology information


alpha-methylacyl-CoA racemase / alpha-methylacyl-CoA racemase activity / acyl-CoA metabolic process / bile acid metabolic process / protein homodimerization activity
Similarity search - Function
formyl-coa transferase, domain 3 / Crotonobetainyl-coa:carnitine coa-transferase; domain 1 / CoA-transferase family III domain 3 superfamily / formyl-coa transferase, domain 3 / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(R)-IBUPROFENOYL-COENZYME A / (S)-IBUPROFENOYL-COENZYME A / : / Alpha-methylacyl-CoA racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBhaumik, P. / Wierenga, R.K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Catalysis of the 1,1-Proton Transfer by alpha-Methyl-acyl-CoA Racemase Is Coupled to a Movement of the Fatty Acyl Moiety Over a Hydrophobic, Methionine-rich Surface
Authors: Bhaumik, P. / Schmitz, W. / Hassinen, A. / Hiltunen, J.K. / Conzelmann, E. / Wierenga, R.K.
History
DepositionMar 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: probable alpha-methylacyl-CoA racemase MCR
B: probable alpha-methylacyl-CoA racemase MCR
C: probable alpha-methylacyl-CoA racemase MCR
D: probable alpha-methylacyl-CoA racemase MCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,54612
Polymers154,8914
Non-polymers7,6548
Water19,9251106
1
A: probable alpha-methylacyl-CoA racemase MCR
B: probable alpha-methylacyl-CoA racemase MCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2736
Polymers77,4462
Non-polymers3,8274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19300 Å2
ΔGint-66 kcal/mol
Surface area22630 Å2
MethodPISA
2
C: probable alpha-methylacyl-CoA racemase MCR
D: probable alpha-methylacyl-CoA racemase MCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2736
Polymers77,4462
Non-polymers3,8274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19320 Å2
ΔGint-70 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.950, 79.580, 117.430
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
12A
22B
32C
42D

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAASPASPAA2 - 372 - 37
211ALAALAASPASPBB2 - 372 - 37
311ALAALAASPASPCC2 - 372 - 37
411ALAALAASPASPDD2 - 372 - 37
521ARGARGTHRTHRAA52 - 20552 - 205
621ARGARGTHRTHRBB52 - 20552 - 205
721ARGARGTHRTHRCC52 - 20552 - 205
821ARGARGTHRTHRDD52 - 20552 - 205
931PHEPHEGLUGLUAA304 - 321304 - 321
1031PHEPHEGLUGLUBB304 - 321304 - 321
1131PHEPHEGLUGLUCC304 - 321304 - 321
1231PHEPHEGLUGLUDD304 - 321304 - 321
1341TRPTRPALAALAAA326 - 346326 - 346
1441TRPTRPALAALABB326 - 346326 - 346
1541TRPTRPALAALACC326 - 346326 - 346
1641TRPTRPALAALADD326 - 346326 - 346
112ASPASPVALVALAA225 - 301225 - 301
212ASPASPVALVALBB225 - 301225 - 301
312ASPASPVALVALCC225 - 301225 - 301
412ASPASPVALVALDD225 - 301225 - 301

NCS ensembles :
ID
1
2

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Components

#1: Protein
probable alpha-methylacyl-CoA racemase MCR / 2-methylacyl-CoA racemase / 2-arylpropionyl-CoA epimerase


Mass: 38722.801 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: CAB09031 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: GenBank: 2117181, UniProt: O06543*PLUS, alpha-methylacyl-CoA racemase
#2: Chemical
ChemComp-SFC / (S)-IBUPROFENOYL-COENZYME A / [5-(6-AMINOPURIN-9-YL)-2-[[[[3-[2-(2-(S)-2-[4-(2-METHYLPROPYL)PHENYL] PROPANOYL)-SULFANYLETHYLCARBAMOYL ETHYLCARBAMOYL]-3-HYDROXY-2,2-DIMETHYL-PROPOXY]-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXYMETHYL]-4-HYDROXY-OXOLAN-3-YL]OXYPHOSPHONIC ACID


Mass: 956.808 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H53N7O17P3S
#3: Chemical
ChemComp-RFC / (R)-IBUPROFENOYL-COENZYME A / [5-(6-AMINOPURIN-9-YL)-2-[[[[3-[2-(2-(R)-2-[4-(2-METHYLPROPYL)PHENYL] PROPANOYL)-SULFANYLETHYLCARBAMOYL ETHYLCARBAMOYL]-3-HYDROXY-2,2-DIMETHYL-PROPOXY]-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXYMETHYL]-4-HYDROXY-OXOLAN-3- YL]OXYPHOSPHONIC ACID


Mass: 956.808 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H53N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1106 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSFC AND RFC ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.52M Ammonium phosphate, 10mM Barium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 10, 2005 / Details: mirrors
RadiationMonochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.85→35 Å / Num. obs: 134349 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 13.5
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.7 / Num. unique all: 9101 / % possible all: 84.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X74

1x74


Resolution: 1.85→19.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.796 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.152 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24644 6719 5 %RANDOM
Rwork0.202 ---
all0.20461 127524 --
obs0.20238 127524 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.477 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10748 0 496 1106 12350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02111328
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.99415440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83951408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71923.226496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.247151696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.80415104
X-RAY DIFFRACTIONr_chiral_restr0.0930.21660
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028776
X-RAY DIFFRACTIONr_nbd_refined0.2080.26287
X-RAY DIFFRACTIONr_nbtor_refined0.3120.27639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.21150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.257
X-RAY DIFFRACTIONr_mcbond_it0.7131.57172
X-RAY DIFFRACTIONr_mcangle_it1.12211168
X-RAY DIFFRACTIONr_scbond_it1.72934759
X-RAY DIFFRACTIONr_scangle_it2.5674.54272
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A916medium positional0.090.5
12B916medium positional0.080.5
13C916medium positional0.090.5
14D916medium positional0.090.5
21A308medium positional0.180.5
22B308medium positional0.130.5
23C308medium positional0.160.5
24D308medium positional0.150.5
11A818loose positional0.265
12B818loose positional0.225
13C818loose positional0.235
14D818loose positional0.245
21A281loose positional0.275
22B281loose positional0.275
23C281loose positional0.355
24D281loose positional0.265
11A916medium thermal0.622
12B916medium thermal0.612
13C916medium thermal0.62
14D916medium thermal0.582
21A308medium thermal0.572
22B308medium thermal0.662
23C308medium thermal0.742
24D308medium thermal0.672
11A818loose thermal1.3210
12B818loose thermal1.3710
13C818loose thermal1.3210
14D818loose thermal1.2710
21A281loose thermal1.2310
22B281loose thermal1.3110
23C281loose thermal1.410
24D281loose thermal1.4110
LS refinement shellResolution: 1.85→1.949 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.387 896 -
Rwork0.332 17091 -
obs-9101 88.45 %

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