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- PDB-3jw8: Crystal structure of human mono-glyceride lipase -

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Basic information

Entry
Database: PDB / ID: 3jw8
TitleCrystal structure of human mono-glyceride lipase
ComponentsMGLL protein
KeywordsHYDROLASE / alpha-beta hydrolase
Function / homology
Function and homology information


Arachidonate production from DAG / Acyl chain remodeling of DAG and TAG / acylglycerol catabolic process / acylglycerol lipase / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / triglyceride catabolic process / monoacylglycerol lipase activity / arachidonate metabolic process / regulation of sensory perception of pain ...Arachidonate production from DAG / Acyl chain remodeling of DAG and TAG / acylglycerol catabolic process / acylglycerol lipase / monoacylglycerol catabolic process / regulation of endocannabinoid signaling pathway / triglyceride catabolic process / monoacylglycerol lipase activity / arachidonate metabolic process / regulation of sensory perception of pain / phosphatidylcholine lysophospholipase activity / Triglyceride catabolism / regulation of signal transduction / lipid metabolic process / fatty acid biosynthetic process / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / regulation of inflammatory response / inflammatory response / endoplasmic reticulum membrane / protein homodimerization activity / membrane / plasma membrane / cytosol
Similarity search - Function
: / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Lipases, serine active site. / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Monoglyceride lipase / Monoglyceride lipase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBertrand, T. / Auge, F. / Houtmann, J. / Rak, A. / Vallee, F. / Mikol, V. / Berne, P.F. / Michot, N. / Cheuret, D. / Hoornaert, C. / Mathieu, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural basis for human monoglyceride lipase inhibition.
Authors: Bertrand, T. / Auge, F. / Houtmann, J. / Rak, A. / Vallee, F. / Mikol, V. / Berne, P.F. / Michot, N. / Cheuret, D. / Hoornaert, C. / Mathieu, M.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: MGLL protein
B: MGLL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4449
Polymers71,6172
Non-polymers8277
Water9,584532
1
A: MGLL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2815
Polymers35,8081
Non-polymers4734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MGLL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1634
Polymers35,8081
Non-polymers3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: MGLL protein
hetero molecules

A: MGLL protein
hetero molecules

A: MGLL protein
hetero molecules

A: MGLL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,12420
Polymers143,2334
Non-polymers1,89116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area9620 Å2
ΔGint-280 kcal/mol
Surface area45020 Å2
MethodPISA
4
B: MGLL protein
hetero molecules

B: MGLL protein
hetero molecules

B: MGLL protein
hetero molecules

B: MGLL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,65216
Polymers143,2334
Non-polymers1,41812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area7670 Å2
ΔGint-221 kcal/mol
Surface area44390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.588, 126.311, 140.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein MGLL protein / Monoglyceride lipase / isoform CRA_b / cDNA / FLJ96595 / Homo sapiens monoglyceride lipase (MGLL) / mRNA


Mass: 35808.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MGLL, hCG_40840 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q6IBG9, UniProt: Q99685*PLUS, acylglycerol lipase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM MES, 40% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9797, 0.9799, 1.000
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2008
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97991
311
ReflectionResolution: 2.1→73.9 Å / Num. all: 44315 / Num. obs: 44315 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 27.56 Å2 / Rsym value: 0.056 / Net I/σ(I): 18.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 6.5 / Rsym value: 0.149 / % possible all: 97.4

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Processing

Software
NameVersionClassification
DNAdata collection
SHARPphasing
BUSTER2.9.3refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→17.21 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 2230 5.03 %RANDOM
Rwork0.1568 ---
obs-44314 --
Displacement parametersBiso mean: 27.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.2451 Å20 Å20 Å2
2--0.7965 Å20 Å2
3----0.5514 Å2
Refine analyzeLuzzati coordinate error obs: 0.175 Å
Refinement stepCycle: LAST / Resolution: 2.1→17.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 56 532 4992
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.32
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2088 173 5.39 %
Rwork0.1522 3037 -
obs-3210 98.04 %

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