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- PDB-9wlv: The Crystal Structure of Alpha-Beta-fold_hydrolase from Microluna... -

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Basic information

Entry
Database: PDB / ID: 9wlv
TitleThe Crystal Structure of Alpha-Beta-fold_hydrolase from Microlunatus sagamiharensis.
ComponentsPimeloyl-ACP methyl ester carboxylesterase
KeywordsHYDROLASE
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / (3R)-3-hydroxybutanoic acid / 4-HYDROXYPHENYLACETATE / Pimeloyl-ACP methyl ester carboxylesterase
Function and homology information
Biological speciesMicrolunatus sagamiharensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHuang, J. / Smith, S. / Wang, Q. / Bao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The Crystal Structure of Alpha-Beta-fold_hydrolase from Microlunatus sagamiharensis.
Authors: Huang, J. / Smith, S. / Wang, Q. / Bao, X.
History
DepositionSep 2, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Pimeloyl-ACP methyl ester carboxylesterase
BBB: Pimeloyl-ACP methyl ester carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,79516
Polymers60,4222
Non-polymers1,37314
Water11,422634
1
AAA: Pimeloyl-ACP methyl ester carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,14311
Polymers30,2111
Non-polymers93210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Pimeloyl-ACP methyl ester carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6515
Polymers30,2111
Non-polymers4404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.212, 125.212, 79.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11AAA-301-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 0 - 289 / Label seq-ID: 1 - 290

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Pimeloyl-ACP methyl ester carboxylesterase


Mass: 30211.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microlunatus sagamiharensis (bacteria) / Gene: SAMN04488544_1883 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H2MDS2

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Non-polymers , 6 types, 648 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-4HP / 4-HYDROXYPHENYLACETATE


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-3HR / (3R)-3-hydroxybutanoic acid


Mass: 104.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris pH6.1, 1.8M (NH4)2SO4 + 0.25% 1,3,5-Pentanetricarboxylic acid, 0.25% 4-Hydroxyphenylacetic acid, 0.25% Benzoic acid, 0.25% Poly(3-hydroxybutyric acid),0.02 M HEPES Na pH6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.953729 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953729 Å / Relative weight: 1
ReflectionResolution: 1.9→49.288 Å / Num. obs: 50439 / % possible obs: 100 % / Redundancy: 25.2 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 21.6
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.986 / Num. unique obs: 3188

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→49.288 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.418 / SU ML: 0.071 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1794 2527 5.016 %
Rwork0.144 47850 -
all0.146 --
obs-50377 99.988 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.733 Å2
Baniso -1Baniso -2Baniso -3
1-0.437 Å2-0 Å2-0 Å2
2--0.437 Å2-0 Å2
3----0.873 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 88 634 4970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134455
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174189
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.636076
X-RAY DIFFRACTIONr_angle_other_deg1.5111.5779605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.27720230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06215627
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6641546
X-RAY DIFFRACTIONr_chiral_restr0.0820.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
X-RAY DIFFRACTIONr_nbd_refined0.2160.2953
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.24123
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22177
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22239
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2465
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2190.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1130.26
X-RAY DIFFRACTIONr_nbd_other0.1290.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.230
X-RAY DIFFRACTIONr_mcbond_it2.142.1872330
X-RAY DIFFRACTIONr_mcbond_other2.1322.1862329
X-RAY DIFFRACTIONr_mcangle_it2.8683.2722912
X-RAY DIFFRACTIONr_mcangle_other2.8713.2732913
X-RAY DIFFRACTIONr_scbond_it3.5162.662125
X-RAY DIFFRACTIONr_scbond_other3.5152.6612126
X-RAY DIFFRACTIONr_scangle_it5.2133.8183158
X-RAY DIFFRACTIONr_scangle_other5.2123.823159
X-RAY DIFFRACTIONr_lrange_it6.52443.81419884
X-RAY DIFFRACTIONr_lrange_other6.31643.04719253
X-RAY DIFFRACTIONr_ncsr_local_group_10.1040.058942
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.103560.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.103560.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.2451790.1853472X-RAY DIFFRACTION100
1.949-2.0030.2131670.1713417X-RAY DIFFRACTION100
2.003-2.0610.1731920.1583280X-RAY DIFFRACTION100
2.061-2.1240.2121600.1523232X-RAY DIFFRACTION100
2.124-2.1940.1761440.1433133X-RAY DIFFRACTION100
2.194-2.2710.1881760.1373013X-RAY DIFFRACTION100
2.271-2.3560.1741690.1382896X-RAY DIFFRACTION100
2.356-2.4530.221570.1372801X-RAY DIFFRACTION100
2.453-2.5610.1871430.1332715X-RAY DIFFRACTION100
2.561-2.6860.1521290.1292585X-RAY DIFFRACTION100
2.686-2.8320.1821140.1442482X-RAY DIFFRACTION100
2.832-3.0030.1671250.1352348X-RAY DIFFRACTION100
3.003-3.210.1661290.1442205X-RAY DIFFRACTION100
3.21-3.4670.1971270.1532054X-RAY DIFFRACTION100
3.467-3.7970.1641000.1421906X-RAY DIFFRACTION100
3.797-4.2450.168820.1331746X-RAY DIFFRACTION100
4.245-4.8990.121840.1121531X-RAY DIFFRACTION100
4.899-5.9960.149560.1571348X-RAY DIFFRACTION100
5.996-8.460.227580.1711055X-RAY DIFFRACTION100
8.46-49.2880.251360.171631X-RAY DIFFRACTION99.1085

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