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- PDB-7v3k: crystal structure of MAJ1 -

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Basic information

Entry
Database: PDB / ID: 7v3k
Titlecrystal structure of MAJ1
ComponentsPutative lipase
KeywordsLIPID BINDING PROTEIN
Function / homologyLipase EstA/Esterase EstB / Lipase (class 2) / lipid catabolic process / Alpha/Beta hydrolase fold / hydrolase activity / OLEIC ACID / Putative lipase
Function and homology information
Biological speciesJanibacter sp. HTCC2649 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsWang, Y.H. / Cui, R.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: crystal structure of MAJ1
Authors: Wang, Y.H. / Cui, R.G.
History
DepositionAug 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative lipase
C: Putative lipase
D: Putative lipase
B: Putative lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,28822
Polymers132,1284
Non-polymers3,16018
Water10,503583
1
A: Putative lipase
B: Putative lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,99213
Polymers66,0642
Non-polymers1,92911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-40 kcal/mol
Surface area21100 Å2
MethodPISA
2
D: Putative lipase
hetero molecules

C: Putative lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2959
Polymers66,0642
Non-polymers1,2327
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area4410 Å2
ΔGint-23 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.864, 114.864, 264.506
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

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Protein / Sugars , 2 types, 8 molecules ACDB

#1: Protein
Putative lipase


Mass: 33031.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Janibacter sp. HTCC2649 (bacteria) / Gene: JNB_12713 / Production host: Escherichia coli (E. coli) / References: UniProt: A3TMR7
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 597 molecules

#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.35 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20%PEG3350,200mM potassium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 60324 / % possible obs: 96.1 % / Redundancy: 9.6 % / Biso Wilson estimate: 34.92 Å2 / CC1/2: 0.917 / Rmerge(I) obs: 0.33 / Rpim(I) all: 0.109 / Net I/σ(I): 10
Reflection shellResolution: 2.49→2.54 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 2958 / Rpim(I) all: 0.311 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H6G

5h6g


Resolution: 2.49→22.89 Å / SU ML: 0.3137 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 2983 4.98 %
Rwork0.1871 56887 -
obs0.1897 59870 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.22 Å2
Refinement stepCycle: LAST / Resolution: 2.49→22.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8698 0 207 579 9484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829120
X-RAY DIFFRACTIONf_angle_d1.141212467
X-RAY DIFFRACTIONf_chiral_restr0.06541425
X-RAY DIFFRACTIONf_plane_restr0.00741633
X-RAY DIFFRACTIONf_dihedral_angle_d10.67941385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.530.34741380.2712465X-RAY DIFFRACTION88.93
2.53-2.570.30791400.2632710X-RAY DIFFRACTION96.81
2.57-2.620.34011420.24592729X-RAY DIFFRACTION96.83
2.62-2.670.30611210.24182737X-RAY DIFFRACTION96.88
2.67-2.720.31181250.23652708X-RAY DIFFRACTION96.95
2.72-2.780.28251640.23182676X-RAY DIFFRACTION96.83
2.78-2.850.28771220.23112748X-RAY DIFFRACTION96.67
2.85-2.920.30811540.22972699X-RAY DIFFRACTION96.65
2.92-30.30131300.21932746X-RAY DIFFRACTION96.87
3-3.090.29771520.21562699X-RAY DIFFRACTION96.81
3.09-3.190.26051520.20852747X-RAY DIFFRACTION96.63
3.19-3.30.25251320.21082717X-RAY DIFFRACTION96.64
3.3-3.430.24911290.18962739X-RAY DIFFRACTION96.37
3.43-3.590.22991520.19052730X-RAY DIFFRACTION96.29
3.59-3.770.23431340.17412743X-RAY DIFFRACTION96.16
3.77-4.010.18951380.16372740X-RAY DIFFRACTION95.81
4.01-4.320.22971550.15312714X-RAY DIFFRACTION95.38
4.32-4.750.19141570.13972710X-RAY DIFFRACTION94.75
4.75-5.430.20191550.14892741X-RAY DIFFRACTION94.18
5.43-6.810.22411380.16732722X-RAY DIFFRACTION92.32
6.81-22.890.17521530.15882667X-RAY DIFFRACTION85.95

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