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- PDB-7dbl: Acyl-CoA hydrolase MpaH' mutant S139A in complex with MPA -

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Basic information

Entry
Database: PDB / ID: 7dbl
TitleAcyl-CoA hydrolase MpaH' mutant S139A in complex with MPA
Componentsacyl-CoA hydrolase MpaH'
KeywordsHYDROLASE / peroxisomal acyl-CoA hydrolase / MpaH' / MPA biosynthesis
Function / homologyMYCOPHENOLIC ACID
Function and homology information
Biological speciesPenicillium brevicompactum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,0748
Polymers196,7934
Non-polymers1,2814
Water15,655869
1
A: acyl-CoA hydrolase MpaH'
B: acyl-CoA hydrolase MpaH'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0374
Polymers98,3972
Non-polymers6412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-36 kcal/mol
Surface area31510 Å2
MethodPISA
2
C: acyl-CoA hydrolase MpaH'
D: acyl-CoA hydrolase MpaH'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0374
Polymers98,3972
Non-polymers6412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-37 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.819, 92.785, 160.756
Angle α, β, γ (deg.)90.000, 95.390, 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:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPROAA3 - 4193 - 419
21THRTHRPROPROBB3 - 4193 - 419
12THRTHRPROPROAA3 - 4193 - 419
22THRTHRPROPROCC3 - 4193 - 419
13METMETSERSERAA1 - 4221 - 422
23METMETSERSERDD1 - 4221 - 422
14THRTHRILEILEBB3 - 4203 - 420
24THRTHRILEILECC3 - 4203 - 420
15THRTHRPROPROBB3 - 4193 - 419
25THRTHRPROPRODD3 - 4193 - 419
16THRTHRPROPROCC3 - 4193 - 419
26THRTHRPROPRODD3 - 4193 - 419

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
acyl-CoA hydrolase MpaH'


Mass: 49198.270 Da / Num. of mol.: 4 / Mutation: S139A
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: Chemical
ChemComp-MOA / MYCOPHENOLIC ACID / 6-(1,3-DIHYDRO-7-HYDROXY-5-METHOXY-4-METHYL-1-OXOISOBENZOFURAN-6-YL)-4-METHYL-4-HEXANOIC ACID


Mass: 320.337 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H20O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 51.2 % / 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: 1.84→48.12 Å / Num. obs: 162262 / % possible obs: 99.4 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.069 / Net I/σ(I): 13.9
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
1.84-1.8820.5511485674940.6720.5510.7791.793
10.1-48.081.90.0121946104910.0120.01747.198.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DBI

7dbi


Resolution: 1.84→48.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.033 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 8119 5 %RANDOM
Rwork0.1791 ---
obs0.1804 154120 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.84 Å2 / Biso mean: 25.45 Å2 / Biso min: 13.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20.59 Å2
2--0.77 Å2-0 Å2
3----1.87 Å2
Refinement stepCycle: final / Resolution: 1.84→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13404 0 92 869 14365
Biso mean--41.49 31.38 -
Num. residues----1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01313859
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712832
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.66118868
X-RAY DIFFRACTIONr_angle_other_deg1.3671.58129743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26851673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9621.041759
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.258152292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.64115120
X-RAY DIFFRACTIONr_chiral_restr0.0810.21794
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022964
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A137870.08
12B137870.08
21A138270.07
22C138270.07
31A140200.06
32D140200.06
41B139590.05
42C139590.05
51B135990.08
52D135990.08
61C136290.08
62D136290.08
LS refinement shellResolution: 1.843→1.891 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 612 -
Rwork0.285 10859 -
all-11471 -
obs--95.08 %

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