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- PDB-4s2f: Joint X-ray/neutron structure of Trichoderma reesei xylanase II a... -

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Basic information

Entry
Database: PDB / ID: 4s2f
TitleJoint X-ray/neutron structure of Trichoderma reesei xylanase II at pH 4.4
ComponentsEndo-1,4-beta-xylanase 2
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / 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 11/12, catalytic domain / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / 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: 1.7 Å
AuthorsKovalevsky, A. / 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 1.4Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.5Jun 20, 2018Group: Data collection / Category: diffrn_radiation / diffrn_source
Item: _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list
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
Revision 2.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Endo-1,4-beta-xylanase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9652
Polymers20,8381
Non-polymers1271
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.963, 59.621, 70.588
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 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


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: PEG8000, 0.1M NaOAc, 0.2M NaI, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12911
22911
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54
NUCLEAR REACTORORNL Spallation Neutron Source MANDI22-4
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV++1IMAGE PLATEMar 12, 2014OSMIC VARIMAX
ANGER CAMERA/ORNL2AREA DETECTORApr 14, 2014
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1noneSINGLE WAVELENGTHMx-ray1
2noneLAUELneutron1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541
221
341
Reflection

Entry-ID: 4S2F

Resolution (Å)Num. obs% possible obs (%)Observed criterion σ(I)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.7-402279695.140.027139.8
2-501389990.61.64.80.25326.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.7640.3432.7191.7
2-2.112.70.2713.2284.2

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Processing

Software
NameVersionClassificationNB
nCNS1.0.0refinement
HKL-3000FOR X-RAYdata collection
MantidFOR NEUTRONdata reduction
HKL-3000FOR X-RAYdata reduction
HKL-3000FOR X-RAYdata scaling
CNSphasing
Refinement

Biso max: 78.54 Å2 / Biso mean: 28.71 Å2 / Biso min: 12.57 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-IDBsol (Å2)ksol (e/Å3)
1.7-29.81X-RAY DIFFRACTION0.2110.0070.199951180572382919008579.81136.5460.487167
2-9.89NEUTRON DIFFRACTION0.3040.0120.2616361241214645130484.989.1250.2360.664436
Refine analyze
Refine-ID#notag 0
X-RAY DIFFRACTION
FreeObs
Luzzati coordinate error0.190.18
Luzzati d res low-5
Luzzati sigma a0.10.11
Luzzati d res high-1.7
NEUTRON DIFFRACTION
FreeObs
Luzzati coordinate error0.360.33
Luzzati d res low-5
Luzzati sigma a0.640.62
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: 1.7→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 1 146 1627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d15.7
X-RAY DIFFRACTIONx_improper_angle_d2.01
NEUTRON DIFFRACTIONx_bond_d0.007
NEUTRON DIFFRACTIONx_angle_deg1.2
NEUTRON DIFFRACTIONx_dihedral_angle_d15.7
NEUTRON DIFFRACTIONx_improper_angle_d2.01
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 (%)
1.7-1.780.213656.50.209941X-RAY DIFFRACTION0.0262940100634.2
1.78-1.870.218854.60.2081746X-RAY DIFFRACTION0.0242926183162.6
1.87-1.990.1911205.20.1932196X-RAY DIFFRACTION0.0172949231678.5
1.99-2.140.22412550.22389X-RAY DIFFRACTION0.022941251485.5
2.14-2.360.2241425.30.2072531X-RAY DIFFRACTION0.0192957267390.4
2.36-2.70.2271515.50.2112593X-RAY DIFFRACTION0.0182973274492.3
2.7-3.40.2031364.70.2012745X-RAY DIFFRACTION0.0173015288195.6
3.4-29.810.2041274.20.192916X-RAY DIFFRACTION0.0183153304396.5
2-2.090.454664.60.3771359NEUTRON DIFFRACTION0.0561793142579.5
2.09-2.20.371895.80.3821446NEUTRON DIFFRACTION0.0391813153584.7
2.2-2.340.382744.70.3511510NEUTRON DIFFRACTION0.0441799158488
2.34-2.510.3581056.30.3331549NEUTRON DIFFRACTION0.0351816165491.1
2.51-2.760.319895.30.291583NEUTRON DIFFRACTION0.0341811167292.3
2.76-3.150.302804.60.2471655NEUTRON DIFFRACTION0.0341844173594.1
3.15-3.930.222573.20.1841703NEUTRON DIFFRACTION0.0291858176094.7
3.93-9.890.217764.50.191607NEUTRON DIFFRACTION0.0251928168387.3

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