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- PDB-1vlq: Crystal structure of Acetyl xylan esterase (TM0077) from Thermoto... -

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Basic information

Entry
Database: PDB / ID: 1vlq
TitleCrystal structure of Acetyl xylan esterase (TM0077) from Thermotoga maritima at 2.10 A resolution
Componentsacetyl xylan esterase
KeywordsHYDROLASE / TM0077 / ACETYL XYLAN ESTERASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


xylan metabolic process / cephalosporin C metabolic process / cephalosporin-C deacetylase / cephalosporin-C deacetylase activity / polysaccharide metabolic process / acetylxylan esterase / acetylxylan esterase activity / carboxylic ester hydrolase activity / cellulose catabolic process / calcium ion binding / cytoplasm
Similarity search - Function
Acetyl xylan esterase / Carbohydrate esterase 7 family / Acetyl xylan esterase (AXE1) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cephalosporin-C deacetylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2012
Title: Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima.
Authors: Levisson, M. / Han, G.W. / Deller, M.C. / Xu, Q. / Biely, P. / Hendriks, S. / Ten Eyck, L.F. / Flensburg, C. / Roversi, P. / Miller, M.D. / McMullan, D. / von Delft, F. / Kreusch, A. / ...Authors: Levisson, M. / Han, G.W. / Deller, M.C. / Xu, Q. / Biely, P. / Hendriks, S. / Ten Eyck, L.F. / Flensburg, C. / Roversi, P. / Miller, M.D. / McMullan, D. / von Delft, F. / Kreusch, A. / Deacon, A.M. / van der Oost, J. / Lesley, S.A. / Elsliger, M.A. / Kengen, S.W. / Wilson, I.A.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 23, 2012Group: Database references
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_leaving_atom_flag / _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: acetyl xylan esterase
B: acetyl xylan esterase
C: acetyl xylan esterase
D: acetyl xylan esterase
E: acetyl xylan esterase
F: acetyl xylan esterase
G: acetyl xylan esterase
H: acetyl xylan esterase
I: acetyl xylan esterase
J: acetyl xylan esterase
K: acetyl xylan esterase
L: acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,98613
Polymers467,89412
Non-polymers921
Water44,3892464
1
A: acetyl xylan esterase
B: acetyl xylan esterase
C: acetyl xylan esterase
D: acetyl xylan esterase
E: acetyl xylan esterase
F: acetyl xylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,0397
Polymers233,9476
Non-polymers921
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19110 Å2
ΔGint-129 kcal/mol
Surface area63100 Å2
MethodPISA
2
G: acetyl xylan esterase
H: acetyl xylan esterase
I: acetyl xylan esterase
J: acetyl xylan esterase
K: acetyl xylan esterase
L: acetyl xylan esterase


Theoretical massNumber of molelcules
Total (without water)233,9476
Polymers233,9476
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18860 Å2
ΔGint-129 kcal/mol
Surface area63400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.640, 130.952, 157.815
Angle α, β, γ (deg.)90.00, 118.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: PHE / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 4 - 320 / Label seq-ID: 16 - 332

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

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Components

#1: Protein
acetyl xylan esterase


Mass: 38991.184 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0077 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXT2, cephalosporin-C deacetylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2464 / 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: 2.93 Å3/Da / Density % sol: 57.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2
Details: 20% PEG-300, 10% glycerol, 0.1M Phosphate-citrate pH 4.2 0.2 M (NH4)2SO4 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL9-210.91837
SYNCHROTRONSSRL BL9-220.918370,0.979126
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9791261
ReflectionResolution: 2.1→29.56 Å / Num. obs: 293140 / % possible obs: 93 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.49 Å2 / Rsym value: 0.09 / Net I/σ(I): 9.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 30908 / Rsym value: 0.433 / % possible all: 67.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHARPphasing
autoSHARPphasing
SHELXmodel building
WARPmodel building
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
SHELXphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.076 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.17
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE ACTIVE SITE TRIAD CONSISTS OF SER188, HIS303 AND ASP274. THE ELECTRON DENSITY SUGGESTED THERE COULD EXIST A PARTIALLY OCCUPIED ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE ACTIVE SITE TRIAD CONSISTS OF SER188, HIS303 AND ASP274. THE ELECTRON DENSITY SUGGESTED THERE COULD EXIST A PARTIALLY OCCUPIED ACYL INTERMEDIATE ON SER188. HOWEVER, IT IS NOT CONCLUSIVE. AS A RESULT, WATER MOLECULES WERE MODELLED. 3. THERE IS SOME UNEXPLAINED DENSITY NEAR N-TERMINUS 4. RESIDUES 134,135 OF CHAIN D,H,I,J,K,L HAVE POOR DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.22336 14726 5 %RANDOM
Rwork0.18354 ---
obs0.18554 278371 92.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.959 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å2-0.82 Å2
2--2.25 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31173 0 6 2464 33643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02232148
X-RAY DIFFRACTIONr_bond_other_d0.0020.0228509
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.93943596
X-RAY DIFFRACTIONr_angle_other_deg0.927366214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30853852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.54923.0731585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.046155085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.37315225
X-RAY DIFFRACTIONr_chiral_restr0.0850.24439
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0236073
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027284
X-RAY DIFFRACTIONr_nbd_refined0.2060.26254
X-RAY DIFFRACTIONr_nbd_other0.1930.228475
X-RAY DIFFRACTIONr_nbtor_other0.0850.216852
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.22055
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.230
X-RAY DIFFRACTIONr_mcbond_it2.176320879
X-RAY DIFFRACTIONr_mcbond_other0.19837800
X-RAY DIFFRACTIONr_mcangle_it2.593531023
X-RAY DIFFRACTIONr_scbond_it4.775814761
X-RAY DIFFRACTIONr_scangle_it6.0351112573
X-RAY DIFFRACTIONr_nbtor_refined0.1880.215311
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1852tight positional0.040.05
2B1852tight positional0.040.05
3C1852tight positional0.040.05
4D1852tight positional0.040.05
5E1852tight positional0.040.05
6F1852tight positional0.040.05
7G1852tight positional0.040.05
8H1852tight positional0.040.05
9I1852tight positional0.040.05
10J1852tight positional0.040.05
11K1852tight positional0.040.05
12L1852tight positional0.040.05
1A2980medium positional0.260.5
2B2980medium positional0.210.5
3C2980medium positional0.220.5
4D2980medium positional0.210.5
5E2980medium positional0.240.5
6F2980medium positional0.220.5
7G2980medium positional0.210.5
8H2980medium positional0.210.5
9I2980medium positional0.220.5
10J2980medium positional0.270.5
11K2980medium positional0.30.5
12L2980medium positional0.270.5
1A1852tight thermal0.160.5
2B1852tight thermal0.20.5
3C1852tight thermal0.20.5
4D1852tight thermal0.160.5
5E1852tight thermal0.150.5
6F1852tight thermal0.160.5
7G1852tight thermal0.160.5
8H1852tight thermal0.190.5
9I1852tight thermal0.160.5
10J1852tight thermal0.180.5
11K1852tight thermal0.180.5
12L1852tight thermal0.20.5
1A2980medium thermal0.982
2B2980medium thermal1.022
3C2980medium thermal1.052
4D2980medium thermal0.922
5E2980medium thermal0.962
6F2980medium thermal0.92
7G2980medium thermal0.952
8H2980medium thermal1.022
9I2980medium thermal0.912
10J2980medium thermal1.012
11K2980medium thermal1.072
12L2980medium thermal1.12
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 727 5.05 %
Rwork0.298 13660 -
obs--61.72 %

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