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- PDB-4s2d: Joint X-ray/neutron structure of Trichoderma reesei xylanase II i... -

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Basic information

Entry
Database: PDB / ID: 4s2d
TitleJoint X-ray/neutron structure of Trichoderma reesei xylanase II in complex with MES at pH 5.7
ComponentsEndo-1,4-beta-xylanase 2Xylanase
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DEUTERATED WATER / IODIDE ION / Endo-1,4-beta-xylanase 2
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKovalevsky, A.Y. / Wan, Q. / Langan, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.
Authors: Wan, Q. / Parks, J.M. / Hanson, B.L. / Fisher, S.Z. / Ostermann, A. / Schrader, T.E. / Graham, D.E. / Coates, L. / Langan, P. / Kovalevsky, A.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Dec 2, 2015Group: Atomic model
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1613
Polymers20,8381
Non-polymers3222
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.174, 60.214, 70.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endo-1,4-beta-xylanase 2 / Xylanase / Xylanase 2 / 1 / 4-beta-D-xylan xylanohydrolase 2


Mass: 20838.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoderma reesei (fungus) / References: UniProt: P36217, endo-1,4-beta-xylanase
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.5M MES, 0.2M NaI, PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 6.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22911
Diffraction source
SourceBeamlineTypeIDWavelength (Å)Wavelength
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORPCSOTHER20.7-6.0
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEOct 10, 2009OSMIC VARIMAX
3HE POSITION SENSITIVE DETECTOR2AREA DETECTORFeb 2, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1noneSINGLE WAVELENGTHMx-ray1
2noneneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
20.71
361
Reflection

Entry-ID: 4S2D

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.55-403040297.940.046122.2
2-22.851239885.51.43.30.22325
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.55-1.612.40.2034.6183.4
2-2.1120.3691.6272.7

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Processing

Software
NameVersionClassificationNB
nCNS1.0.0refinement
HKL-2000FOR X-RAYdata collection
d*TREKFOR NEUTRONdata scaling
HKL-2000FOR X-RAYdata reduction
d*TREKFOR NEUTRONdata reduction
HKL-2000FOR X-RAYdata scaling
CNSphasing
Refinement

Biso max: 76.77 Å2 / Biso mean: 22.77 Å2 / Biso min: 10.1 Å2 / R Free selection details: RANDOM / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Stereochemistry target values: JOINT X-RAY/NEUTRON ML / Solvent model: CNS BULK SOLVENT MODEL USED

Resolution (Å)Refine-IDRfactor RfreeRfactor Rfree errorRfactor RworkNum. reflection RfreeNum. reflection RworkNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDBsol2)ksol (e/Å3)
1.6-19.99X-RAY DIFFRACTION0.1960.0050.19213512539328247267445.194.7145.0840.306471
2-19.99NEUTRON DIFFRACTION0.2790.0110.243588111011465811689579.7236.54050.630218
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.180.17
Luzzati d res low-5
Luzzati sigma a0.10.1
Luzzati d res high-1.6
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.340.3
Luzzati d res low-5
Luzzati sigma a0.640.55
Luzzati d res high-2
Refine funct minimized
Refine-IDType
X-RAY DIFFRACTIONJOINT X-RAY/NEUTRON ML
NEUTRON DIFFRACTIONJOINT X-RAY/NEUTRON ML
Refinement stepCycle: LAST / Resolution: 1.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 13 151 1644
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_improper_angle_d2.62
NEUTRON DIFFRACTIONx_bond_d0.01
NEUTRON DIFFRACTIONx_angle_deg1
NEUTRON DIFFRACTIONx_dihedral_angle_d23.5
NEUTRON DIFFRACTIONx_improper_angle_d2.62
LS refinement shell

Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRefine-IDRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.6-1.670.251545.30.2482734X-RAY DIFFRACTION0.023485288882.9
1.67-1.760.2191414.50.2222960X-RAY DIFFRACTION0.0183481310189.1
1.76-1.870.2091705.20.23098X-RAY DIFFRACTION0.0163484326893.8
1.87-2.020.2081755.20.1983205X-RAY DIFFRACTION0.0163518338096.1
2.02-2.220.2071785.20.2053244X-RAY DIFFRACTION0.0153507342297.6
2.22-2.540.2141815.30.2113264X-RAY DIFFRACTION0.0163516344598
2.54-3.20.2311654.60.2063386X-RAY DIFFRACTION0.0183577355199.2
3.2-19.990.1541875.10.1613502X-RAY DIFFRACTION0.0113719368999.2
2-2.090.392625.50.3741060NEUTRON DIFFRACTION0.051802112262.3
2.09-2.20.36625.10.3571146NEUTRON DIFFRACTION0.0461796120867.3
2.2-2.340.353665.10.3151228NEUTRON DIFFRACTION0.0431819129471.1
2.34-2.520.314765.60.3011283NEUTRON DIFFRACTION0.0361802135975.4
2.52-2.770.335704.70.2831424NEUTRON DIFFRACTION0.041824149481.9
2.77-3.170.302684.30.2491528NEUTRON DIFFRACTION0.0371832159687.1
3.17-3.990.211965.50.1721647NEUTRON DIFFRACTION0.0221847174394.4
3.99-19.990.191884.70.1621785NEUTRON DIFFRACTION0.021951187396

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