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- PDB-4dev: An Acetyl Xylan Esterase (Est2A) from the Rumen Bacterium Butyriv... -

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Basic information

Entry
Database: PDB / ID: 4dev
TitleAn Acetyl Xylan Esterase (Est2A) from the Rumen Bacterium Butyrivibrio proteoclasticus.
ComponentsAcetyl-xylan esterase Est2A
KeywordsHYDROLASE / acetyl xylan esterase
Function / homology
Function and homology information


carboxylic ester hydrolase activity
Similarity search - Function
CtCE2-like domain / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Galactose-binding domain-like / Jelly Rolls / Sandwich / Rossmann fold ...CtCE2-like domain / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Galactose-binding domain-like / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DI(HYDROXYETHYL)ETHER / Acetyl-xylan esterase Est2A
Similarity search - Component
Biological speciesButyrivibrio proteoclasticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTill, M. / Arcus, V.L.
CitationJournal: Proteins / Year: 2013
Title: Structure and function of an acetyl xylan esterase (Est2A) from the rumen bacterium Butyrivibrio proteoclasticus.
Authors: Till, M. / Goldstone, D.C. / Attwood, G.T. / Moon, C.D. / Kelly, W.J. / Arcus, V.L.
History
DepositionJan 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Acetyl-xylan esterase Est2A
B: Acetyl-xylan esterase Est2A
C: Acetyl-xylan esterase Est2A
D: Acetyl-xylan esterase Est2A
E: Acetyl-xylan esterase Est2A
F: Acetyl-xylan esterase Est2A
G: Acetyl-xylan esterase Est2A
H: Acetyl-xylan esterase Est2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,69838
Polymers369,5348
Non-polymers2,16430
Water30,7521707
1
A: Acetyl-xylan esterase Est2A
C: Acetyl-xylan esterase Est2A
F: Acetyl-xylan esterase Est2A
G: Acetyl-xylan esterase Est2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,84619
Polymers184,7674
Non-polymers1,07815
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-35 kcal/mol
Surface area52920 Å2
MethodPISA
2
B: Acetyl-xylan esterase Est2A
D: Acetyl-xylan esterase Est2A
E: Acetyl-xylan esterase Est2A
H: Acetyl-xylan esterase Est2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,85219
Polymers184,7674
Non-polymers1,08515
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-23 kcal/mol
Surface area53150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.112, 95.786, 98.787
Angle α, β, γ (deg.)89.96, 99.74, 92.50
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

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
11LEULEUPHEPHEAA4 - 37536 - 407
21LEULEUPHEPHEBB4 - 37536 - 407
12LEULEUPHEPHEAA4 - 37536 - 407
22LEULEUPHEPHECC4 - 37536 - 407
13LEULEUTRPTRPAA4 - 37436 - 406
23LEULEUTRPTRPDD4 - 37436 - 406
14LEULEUPHEPHEAA4 - 37536 - 407
24LEULEUPHEPHEEE4 - 37536 - 407
15LEULEUTRPTRPAA4 - 37436 - 406
25LEULEUTRPTRPFF4 - 37436 - 406
16LEULEUTRPTRPAA4 - 37436 - 406
26LEULEUTRPTRPGG4 - 37436 - 406
17LEULEUTRPTRPAA4 - 37436 - 406
27LEULEUTRPTRPHH4 - 37436 - 406
18LEULEUPHEPHEBB4 - 37536 - 407
28LEULEUPHEPHECC4 - 37536 - 407
19LEULEUTRPTRPBB4 - 37436 - 406
29LEULEUTRPTRPDD4 - 37436 - 406
110LEULEUPHEPHEBB4 - 37536 - 407
210LEULEUPHEPHEEE4 - 37536 - 407
111LEULEUTRPTRPBB4 - 37436 - 406
211LEULEUTRPTRPFF4 - 37436 - 406
112LEULEUTRPTRPBB4 - 37436 - 406
212LEULEUTRPTRPGG4 - 37436 - 406
113LEULEUTRPTRPBB4 - 37436 - 406
213LEULEUTRPTRPHH4 - 37436 - 406
114LEULEUTRPTRPCC4 - 37436 - 406
214LEULEUTRPTRPDD4 - 37436 - 406
115LEULEUPHEPHECC4 - 37536 - 407
215LEULEUPHEPHEEE4 - 37536 - 407
116LEULEUTRPTRPCC4 - 37436 - 406
216LEULEUTRPTRPFF4 - 37436 - 406
117LEULEUTRPTRPCC4 - 37436 - 406
217LEULEUTRPTRPGG4 - 37436 - 406
118LEULEUTRPTRPCC4 - 37436 - 406
218LEULEUTRPTRPHH4 - 37436 - 406
119LEULEUTRPTRPDD4 - 37436 - 406
219LEULEUTRPTRPEE4 - 37436 - 406
120VALVALPHEPHEDD3 - 37535 - 407
220VALVALPHEPHEFF3 - 37535 - 407
121VALVALPHEPHEDD3 - 37535 - 407
221VALVALPHEPHEGG3 - 37535 - 407
122VALVALPHEPHEDD3 - 37535 - 407
222VALVALPHEPHEHH3 - 37535 - 407
123LEULEUTRPTRPEE4 - 37436 - 406
223LEULEUTRPTRPFF4 - 37436 - 406
124LEULEUTRPTRPEE4 - 37436 - 406
224LEULEUTRPTRPGG4 - 37436 - 406
125LEULEUTRPTRPEE4 - 37436 - 406
225LEULEUTRPTRPHH4 - 37436 - 406
126VALVALPHEPHEFF3 - 37535 - 407
226VALVALPHEPHEGG3 - 37535 - 407
127VALVALPHEPHEFF3 - 37535 - 407
227VALVALPHEPHEHH3 - 37535 - 407
128VALVALPHEPHEGG3 - 37535 - 407
228VALVALPHEPHEHH3 - 37535 - 407

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Acetyl-xylan esterase Est2A


Mass: 46191.789 Da / Num. of mol.: 8 / Mutation: H351A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Butyrivibrio proteoclasticus (bacteria)
Strain: ATCC 51982 / DSM 14932 / B316 / Gene: est2A, bpr_I2939 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E0RVY7

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Non-polymers , 5 types, 1737 molecules

#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1707 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 289.15 K / pH: 4.6
Details: 16% (w/v) PEG4000, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→98 Å / Num. obs: 215870 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.161 / Rsym value: 0.188 / Net I/σ(I): 6
Reflection shellResolution: 2→2.11 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→97.36 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.037 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22424 10845 5 %RANDOM
Rwork0.19019 ---
obs0.1919 205024 98.22 %-
all-219780 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.406 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å2-0.28 Å20.59 Å2
2---0.88 Å2-0.18 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→97.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23636 0 142 1707 25485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224275
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0721.94932818
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69952972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59725.0461195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.433154126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0115112
X-RAY DIFFRACTIONr_chiral_restr0.0730.23482
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118712
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.171.514835
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.975223784
X-RAY DIFFRACTIONr_scbond_it3.41439420
X-RAY DIFFRACTIONr_scangle_it5.2134.58995
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A5340.06
12B5340.06
21A5410.06
22C5410.06
31A5180.04
32D5180.04
41A5340.07
42E5340.07
51A5230.04
52F5230.04
61A5260.06
62G5260.06
71A5190.06
72H5190.06
81B5370.07
82C5370.07
91B5190.04
92D5190.04
101B5270.06
102E5270.06
111B5210.04
112F5210.04
121B5230.06
122G5230.06
131B5200.07
132H5200.07
141C5230.05
142D5230.05
151C5360.06
152E5360.06
161C5250.04
162F5250.04
171C5330.05
172G5330.05
181C5240.05
182H5240.05
191D5190.07
192E5190.07
201D5320
202F5320
211D5270.04
212G5270.04
221D5250.05
222H5250.05
231E5200.05
232F5200.05
241E5250.04
242G5250.04
251E5190.05
252H5190.05
261F5290.04
262G5290.04
271F5320.05
272H5320.05
281G5330.05
282H5330.05
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 807 -
Rwork0.247 14985 -
obs--97.28 %

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