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- PDB-1w91: crystal structure of 1,4-BETA-D-XYLAN XYLOHYDROLASE solve using a... -

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Basic information

Entry
Database: PDB / ID: 1w91
Titlecrystal structure of 1,4-BETA-D-XYLAN XYLOHYDROLASE solve using anomalous signal from Seleniomethionine
ComponentsBETA-XYLOSIDASEXylan 1,4-b-xylosidase
KeywordsHYDROLASE / XYLOSIDASE / MAD / SEMET / TETRAMER
Function / homology
Function and homology information


xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process
Similarity search - Function
Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Glycosyl hydrolase domain; family 39 / : / : / Glycosyl hydrolases family 39 active site. / Glycoside hydrolase, family 39 / Glycosyl hydrolases family 39 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsJakoncic, J. / Shoham, G. / Stojanoff, V.
CitationJournal: To be Published
Title: Crystal Structure of 1,4-Beta-D-Xylan Xylohydrolase from Geobacillus Stearothermophilus.
Authors: Jakoncic, J. / Shoham, G. / Stojanoff, V.
History
DepositionOct 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA, CA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 8-STRANDED BARRELS REPRESENTED BY 9-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA, EA, FA, GA, HB " IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS REPRESENTED BY 8-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-XYLOSIDASE
B: BETA-XYLOSIDASE
C: BETA-XYLOSIDASE
D: BETA-XYLOSIDASE
E: BETA-XYLOSIDASE
F: BETA-XYLOSIDASE
G: BETA-XYLOSIDASE
H: BETA-XYLOSIDASE


Theoretical massNumber of molelcules
Total (without water)465,2088
Polymers465,2088
Non-polymers00
Water52,0452889
1
A: BETA-XYLOSIDASE
B: BETA-XYLOSIDASE
C: BETA-XYLOSIDASE
D: BETA-XYLOSIDASE


Theoretical massNumber of molelcules
Total (without water)232,6044
Polymers232,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: BETA-XYLOSIDASE
F: BETA-XYLOSIDASE
G: BETA-XYLOSIDASE
H: BETA-XYLOSIDASE


Theoretical massNumber of molelcules
Total (without water)232,6044
Polymers232,6044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)93.698, 166.024, 313.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A
14E
24A
15F
25A
16G
26A
17H
27A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B4 - 502
2114A4 - 502
1124C4 - 502
2124A4 - 502
1134D4 - 502
2134A4 - 502
1144E4 - 502
2144A4 - 502
1154F4 - 502
2154A4 - 502
1164G4 - 502
2164A4 - 502
1174H4 - 502
2174A4 - 502

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein
BETA-XYLOSIDASE / Xylan 1,4-b-xylosidase / BETA-D-XYLOSIASE / 1 / 4-BETA-D-XYLAN XYLOHYDROLASE / XYLAN 1 / 4-BETA-XYLOSIDASE


Mass: 58150.988 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) / References: UniProt: Q9ZFM2, EC: 3.1.2.37
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2889 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN CORRESPONDS TO THE UNIPROT ENTRY Q9ZFM2. THE SAMPLE USED IN THE EXPERIMENT HAD AN ...THE PROTEIN CORRESPONDS TO THE UNIPROT ENTRY Q9ZFM2. THE SAMPLE USED IN THE EXPERIMENT HAD AN INSERTION AT POSITION 445 IN THE PDB ENTRY AND THE RESIDUES 249-250 FROM THE UNIPROT ENTRY WERE DELETED. THE DBREF RECORD DESCRIBES THE DELETION AND INSERTION MUTATION. THE SEQADV RECORDS DESCRIBE THE CONFLICTS BETWEEN THE UNIPROT ENTRY Q9ZFM2 AND THE OBSERVED CRYSTAL STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.93
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.2→2.2 Å / Num. obs: 240591 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.2→8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.186 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 11807 5 %RANDOM
Rwork0.174 ---
obs0.177 223893 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32656 0 0 2889 35545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02233576
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9445568
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05953976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52523.4121688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.469155560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.64115232
X-RAY DIFFRACTIONr_chiral_restr0.180.24840
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0225968
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.216189
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.222430
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.22880
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3310.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2991.520499
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.944232288
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.24315236
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9164.513280
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Number: 4082 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Bmedium positional0.240.5
2Cmedium positional0.310.5
3Dmedium positional0.270.5
4Emedium positional0.270.5
5Fmedium positional0.250.5
6Gmedium positional0.280.5
7Hmedium positional0.290.5
1Bmedium thermal0.882
2Cmedium thermal0.992
3Dmedium thermal0.932
4Emedium thermal0.992
5Fmedium thermal1.252
6Gmedium thermal1.152
7Hmedium thermal1.212
LS refinement shellResolution: 2.2→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 780 -
Rwork0.177 15076 -
obs--100 %

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