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- PDB-7dbi: Crystal structure of the peroxisomal acyl-CoA hydrolase MpaH -

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Basic information

Entry
Database: PDB / ID: 7dbi
TitleCrystal structure of the peroxisomal acyl-CoA hydrolase MpaH
Componentsacyl-CoA hydrolase MpaH'
KeywordsHYDROLASE / peroxisomal acyl-CoA hydrolase / MpaH' / MPA biosynthesis
Biological speciesPenicillium brevicompactum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsLi, S.Y. / You, C.
CitationJournal: Febs J. / Year: 2021
Title: Structural basis for substrate specificity of the peroxisomal acyl-CoA hydrolase MpaH' involved in mycophenolic acid biosynthesis.
Authors: You, C. / Li, F. / Zhang, X. / Ma, L. / Zhang, Y.Z. / Zhang, W. / Li, S.
History
DepositionOct 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acyl-CoA hydrolase MpaH'
B: acyl-CoA hydrolase MpaH'
C: acyl-CoA hydrolase MpaH'
D: acyl-CoA hydrolase MpaH'


Theoretical massNumber of molelcules
Total (without water)199,2964
Polymers199,2964
Non-polymers00
Water13,980776
1
A: acyl-CoA hydrolase MpaH'
D: acyl-CoA hydrolase MpaH'


Theoretical massNumber of molelcules
Total (without water)99,6482
Polymers99,6482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-43 kcal/mol
Surface area32150 Å2
MethodPISA
2
B: acyl-CoA hydrolase MpaH'
C: acyl-CoA hydrolase MpaH'


Theoretical massNumber of molelcules
Total (without water)99,6482
Polymers99,6482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-42 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.921, 93.260, 161.275
Angle α, β, γ (deg.)90.000, 95.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUPROPROAA4 - 4194 - 419
221GLUGLUPROPROBB4 - 4194 - 419
132THRTHRSERSERAA3 - 4223 - 422
242THRTHRSERSERCC3 - 4223 - 422
153THRTHRPROPROAA3 - 4193 - 419
263THRTHRPROPRODD3 - 4193 - 419
174GLUGLUPROPROBB4 - 4194 - 419
284GLUGLUPROPROCC4 - 4194 - 419
195GLUGLUPROPROBB4 - 4194 - 419
2105GLUGLUPROPRODD4 - 4194 - 419
1116THRTHRPROPROCC3 - 4193 - 419
2126THRTHRPROPRODD3 - 4193 - 419

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
acyl-CoA hydrolase MpaH'


Mass: 49823.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium brevicompactum (fungus) / Strain: NRRL 864 / Gene: MPA' / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.28 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: Imidazole, Calcium acetate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Dec 7, 2019 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→46.63 Å / Num. obs: 130308 / % possible obs: 99.1 % / Redundancy: 2 % / CC1/2: 0.987 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.094 / Rrim(I) all: 0.133 / Net I/σ(I): 11.9 / Num. measured all: 256693
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.99-2.0220.3031261063670.8730.3030.4282.797.4
10.89-46.631.90.08415608430.9810.0840.11932.198.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→46.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.531 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 6548 5 %RANDOM
Rwork0.1683 ---
obs0.1696 123738 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.73 Å2 / Biso mean: 27.389 Å2 / Biso min: 15.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å20.72 Å2
2--2.49 Å2-0 Å2
3----2.72 Å2
Refinement stepCycle: final / Resolution: 1.99→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13387 0 0 776 14163
Biso mean---32.15 -
Num. residues----1675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313749
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712730
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.65818718
X-RAY DIFFRACTIONr_angle_other_deg1.3011.57229521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95151671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61321.053760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23152141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.69615120
X-RAY DIFFRACTIONr_chiral_restr0.0760.21790
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022957
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A135190.08
12B135190.08
21A138890.06
22C138890.06
31A136550.08
32D136550.08
41B135480.08
42C135480.08
51B136320.07
52D136320.07
61C136730.08
62D136730.08
LS refinement shellResolution: 1.99→2.041 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.248 487 -
Rwork0.231 9040 -
obs--98.23 %

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