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- PDB-7xmj: Crystal structure of carbohydrate esterase family 7 acetyl xylan ... -

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Basic information

Entry
Database: PDB / ID: 7xmj
TitleCrystal structure of carbohydrate esterase family 7 acetyl xylan esterase
ComponentsAcetylxylan esterase
KeywordsSTRUCTURAL PROTEIN / carbohydrate esterase / carbohydrate esterase family 7 / acetyl xylan esterase
Function / homologyAcetyl xylan esterase / Carbohydrate esterase 7 family / Acetyl xylan esterase (AXE1) / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds / Alpha/Beta hydrolase fold / Acetylxylan esterase
Function and homology information
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41066763497 Å
AuthorsJiang, Z.Q. / Ma, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of carbohydrate esterase family 7 acetyl xylan esterase
Authors: Jiang, Z.Q. / Ma, J.W.
History
DepositionApr 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
SupersessionNov 8, 2023ID: 7CUZ
Revision 1.1Nov 8, 2023Group: Advisory / Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_database_PDB_obs_spr
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylxylan esterase
B: Acetylxylan esterase
C: Acetylxylan esterase
D: Acetylxylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,3677
Polymers143,2474
Non-polymers1203
Water5,441302
1
A: Acetylxylan esterase
C: Acetylxylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7034
Polymers71,6232
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-21 kcal/mol
Surface area24930 Å2
MethodPISA
2
B: Acetylxylan esterase
D: Acetylxylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6633
Polymers71,6232
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-15 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.714, 147.714, 135.389
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 8 - 308 / Label seq-ID: 8 - 308

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and (resid 8:10 or (resid 11 and (name...AA
22(chain 'B' and (resid 8:10 or (resid 11 and (name...BB
33(chain 'C' and (resid 8:17 or (resid 18 and (name...CC
44(chain 'D' and (resid 8:10 or (resid 11 and (name...DD

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Components

#1: Protein
Acetylxylan esterase


Mass: 35811.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain KF147) (lactic acid bacteria)
Gene: axe, LLKF_1447 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A9QSE8, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.2M ammonium sulfate, 0.075M MES monohydrate pH 6.5, 7.5% (v/v) 1,4-Dioxane, 25% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.41→35.48 Å / Num. obs: 64479 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 48.835415836 Å2 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.111 / Net I/σ(I): 24.9
Reflection shellResolution: 6.85→49.9146 Å / Rmerge(I) obs: 0.287 / Num. unique obs: 2736

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHENIXmodel building
PHENIXdev_2474refinement
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FCY

3fcy


Resolution: 2.41066763497→35.4797551667 Å / SU ML: 0.346198931596 / Cross valid method: FREE R-VALUE / σ(F): 1.37664785009 / Phase error: 28.9491788545
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.280243235644 3205 4.97076476883 %
Rwork0.248068546542 61272 -
obs0.249672053675 64477 99.8173233222 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.5813405969 Å2
Refinement stepCycle: LAST / Resolution: 2.41066763497→35.4797551667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9756 0 3 302 10061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027240908421710018
X-RAY DIFFRACTIONf_angle_d0.63407949392413600
X-RAY DIFFRACTIONf_chiral_restr0.04520537033831449
X-RAY DIFFRACTIONf_plane_restr0.004264063204121745
X-RAY DIFFRACTIONf_dihedral_angle_d14.08283148235856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4107-2.44660.3046465492121330.2996853976042632X-RAY DIFFRACTION98.6091298146
2.4466-2.48490.3604380028771080.2896948627742662X-RAY DIFFRACTION99.9639119451
2.4849-2.52560.280174178131380.2892806972152642X-RAY DIFFRACTION99.9281092739
2.5256-2.56910.3045964813691370.2852600124232707X-RAY DIFFRACTION99.894625922
2.5691-2.61580.3275680099731600.2879601372832596X-RAY DIFFRACTION99.8912649511
2.6158-2.66610.3558630737011260.2918377894432683X-RAY DIFFRACTION99.6806245564
2.6661-2.72050.3365845089761610.2883592980912629X-RAY DIFFRACTION99.7854077253
2.7205-2.77970.3131963621991490.2867438911262681X-RAY DIFFRACTION99.7532604864
2.7797-2.84430.2775538559841360.2831964208952638X-RAY DIFFRACTION99.963963964
2.8443-2.91540.3233462014611480.2708784950592628X-RAY DIFFRACTION99.9639899172
2.9154-2.99420.3361643294681280.2849694938052681X-RAY DIFFRACTION99.9644128114
2.9942-3.08220.3492737766981190.2832945297822718X-RAY DIFFRACTION100
3.0822-3.18170.2986597918651490.2681765128842645X-RAY DIFFRACTION100
3.1817-3.29530.2776520860181470.2581938019562630X-RAY DIFFRACTION99.9640028798
3.2953-3.42710.2899720185941740.2561039145932630X-RAY DIFFRACTION100
3.4271-3.5830.2933047410711280.2446328360842697X-RAY DIFFRACTION100
3.583-3.77170.2623044773351830.2410823674672617X-RAY DIFFRACTION100
3.7717-4.00770.2668989552341230.2284894223542717X-RAY DIFFRACTION100
4.0077-4.31660.2524416306221260.2226484182382650X-RAY DIFFRACTION99.9639899172
4.3166-4.75010.2461420666181190.2272850788782712X-RAY DIFFRACTION99.8589065256
4.7501-5.43530.2667637422291270.2296763250312690X-RAY DIFFRACTION100
5.4353-6.83990.2953237412731510.237192370032677X-RAY DIFFRACTION99.9646518204
6.8399-35.4790.2338599281071350.2268264798432710X-RAY DIFFRACTION98.6819285467
Refinement TLS params.Method: refined / Origin x: -40.9048605678 Å / Origin y: 14.3563063439 Å / Origin z: -0.49602436209 Å
111213212223313233
T0.466067336846 Å2-0.0171498319921 Å2-0.128298270345 Å2-0.429898750753 Å20.0542039711266 Å2--0.366186128335 Å2
L0.651545482962 °2-0.412144492021 °2-0.0599449733243 °2-0.216631995109 °20.0289209922919 °2---0.11990330182 °2
S-0.0424628213342 Å °0.0176435446847 Å °0.0101221237181 Å °-0.00485283969223 Å °0.00426642696957 Å °0.0246189922889 Å °-0.0519770255067 Å °0.0300519888304 Å °0.0320739172469 Å °
Refinement TLS groupSelection details: all

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