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- PDB-4qi5: Dehydrogenase domain of Myriococcum thermophilum cellobiose dehyd... -

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Basic information

Entry
Database: PDB / ID: 4qi5
TitleDehydrogenase domain of Myriococcum thermophilum cellobiose dehydrogenase with bound cellobionolactam, MtDH
ComponentsCellobiose dehydrogenase
KeywordsOXIDOREDUCTASE / FAD/NAD(P)-binding domain / cellobiose oxidizing / electron transfer / lignocellulose degradation / CDH cytochrome domain / cellobiose / cellobionolactam
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / cellulose binding / polysaccharide catabolic process / flavin adenine dinucleotide binding / extracellular region / metal ion binding
Similarity search - Function
Cellobiose dehydrogenase, cytochrome domain / Cytochrome domain of cellobiose dehydrogenase / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / FAD-dependent oxidoreductase 2, FAD binding domain / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain ...Cellobiose dehydrogenase, cytochrome domain / Cytochrome domain of cellobiose dehydrogenase / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / FAD-dependent oxidoreductase 2, FAD binding domain / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / FAD binding domain / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-ABL / : / FLAVIN-ADENINE DINUCLEOTIDE / Cellobiose dehydrogenase
Similarity search - Component
Biological speciesMyriococcum thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsTan, T.C. / Gandini, R. / Sygmund, C. / Kittl, R. / Haltrich, D. / Ludwig, R. / Hallberg, B.M. / Divne, C.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.
Authors: Tan, T.C. / Kracher, D. / Gandini, R. / Sygmund, C. / Kittl, R. / Haltrich, D. / Hallberg, B.M. / Ludwig, R. / Divne, C.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4307
Polymers63,2311
Non-polymers2,1986
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.324, 171.324, 73.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cellobiose dehydrogenase /


Mass: 63231.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myriococcum thermophilum (fungus) / Strain: CBS 208.89 / Gene: CDH / Plasmid: pPICZ B / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: A9XK88

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-ABL / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside / 5-amino-5-deoxy-cellobiono-1,5-lactam / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucoside / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl D-glucoside / (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl glucoside


Type: D-saccharide / Mass: 339.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H21NO10
IdentifierTypeProgram
5-amino-5-deoxy-cellobiono-1,5-lactamIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 185 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 4.89 Å3/Da / Density % sol: 74.85 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 0.1 M NaAc pH 4.6, 0.1 M CdCl2, 18% (w/v) PEG monomethylether 550, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2010 / Details: MIRRORS
RadiationMonochromator: CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.4→44.472 Å / Num. obs: 47898 / % possible obs: 99.7 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.3_1477)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: DEHYDROGENASE DOMAIN WITHOUT LIGAND

Resolution: 2.4→44.47 Å / SU ML: 0.37 / σ(F): 1.99 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1485 3.1 %
Rwork0.196 --
obs0.198 47891 99.7 %
all-47891 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→44.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 134 182 4772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094713
X-RAY DIFFRACTIONf_angle_d1.3676440
X-RAY DIFFRACTIONf_dihedral_angle_d14.3341645
X-RAY DIFFRACTIONf_chiral_restr0.058713
X-RAY DIFFRACTIONf_plane_restr0.008831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.33131370.2934173X-RAY DIFFRACTION99
2.4775-2.5660.35021240.29394175X-RAY DIFFRACTION100
2.566-2.66880.36711200.2834221X-RAY DIFFRACTION100
2.6688-2.79020.34511340.26524186X-RAY DIFFRACTION100
2.7902-2.93730.31511180.25344230X-RAY DIFFRACTION100
2.9373-3.12130.30851350.24134212X-RAY DIFFRACTION100
3.1213-3.36220.32421450.22494205X-RAY DIFFRACTION100
3.3622-3.70040.23041380.19064206X-RAY DIFFRACTION100
3.7004-4.23550.21171400.16274228X-RAY DIFFRACTION100
4.2355-5.33490.17531450.13374241X-RAY DIFFRACTION100
5.3349-44.48010.18181490.15664329X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0944-0.07720.07630.0318-0.00610.0706-0.01170.06490.1131-0.08250.19310.2141-0.09320.09190.00190.36350.03820.01860.15020.01930.342971.004-20.2259-17.7834
20.4201-0.0883-0.08160.4226-0.23910.5846-0.00270.05260.0548-0.0932-0.00040.0293-0.1069-0.005600.44170.0092-0.01370.17210.00320.248988.758-18.1603-34.0622
3-0.01740.2122-0.09910.6965-0.19790.82490.0064-0.05150.10690.0919-0.03420.0902-0.27290.0503-0.00280.3539-0.00150.00250.1211-0.01030.231983.3282-17.2865-17.7333
40.43730.3192-0.20220.31320.00110.23470.0127-0.07150.0862-0.0224-0.0454-0.2146-0.19730.17550.00030.4333-0.0208-0.03160.23690.0260.3125100.4784-20.4548-28.2468
50.0879-0.1580.1040.2186-0.06040.39420.09760.0112-0.06820.0951-0.137-0.094-0.12750.111800.2663-0.02170.00120.18870.01510.2839100.2211-26.456-24.6139
60.14710.2070.15320.32430.04030.15720.0317-0.1250.06550.0757-0.02920.0625-0.1119-0.065900.293-0.01140.02850.2484-0.02250.253673.849-38.927-6.9147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 223 through 265 )
2X-RAY DIFFRACTION2chain 'A' and (resid 266 through 405 )
3X-RAY DIFFRACTION3chain 'A' and (resid 406 through 566 )
4X-RAY DIFFRACTION4chain 'A' and (resid 567 through 648 )
5X-RAY DIFFRACTION5chain 'A' and (resid 649 through 749 )
6X-RAY DIFFRACTION6chain 'A' and (resid 750 through 807 )

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