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- PDB-4qi4: Dehydrogenase domain of Myriococcum thermophilum cellobiose dehyd... -

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Basic information

Entry
Database: PDB / ID: 4qi4
TitleDehydrogenase domain of Myriococcum thermophilum cellobiose dehydrogenase, MtDH
ComponentsCellobiose dehydrogenase
KeywordsOXIDOREDUCTASE / FAD/NAD(P)-binding domain / cellobiose oxidizing / electron transfer / lignocellulose degradation / CDH cytochrome domain
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 / CBM1 (carbohydrate binding type-1) domain signature. / FAD-dependent oxidoreductase 2, FAD binding domain / 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 / CBM1 (carbohydrate binding type-1) domain signature. / FAD-dependent oxidoreductase 2, FAD binding domain / 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
: / FLAVIN-ADENINE DINUCLEOTIDE / Cellobiose dehydrogenase
Similarity search - Component
Biological speciesMyriococcum thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _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

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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)66,09914
Polymers63,2311
Non-polymers2,86713
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cellobiose dehydrogenase
hetero molecules

A: Cellobiose dehydrogenase
hetero molecules

A: Cellobiose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,29642
Polymers189,6943
Non-polymers8,60239
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area15450 Å2
ΔGint-111 kcal/mol
Surface area59180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.755, 171.755, 72.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-911-

CD

21A-913-

CD

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Components

#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
#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
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd

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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: 4.85 Å3/Da / Density % sol: 74.64 %
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: 2.7→44.32 Å / Num. obs: 33521 / % possible obs: 99.9 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.8.3_1477)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.7→44.32 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1991 5.94 %
Rwork0.181 --
obs0.184 33519 99.9 %
all-33519 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 132 0 4588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014712
X-RAY DIFFRACTIONf_angle_d1.396429
X-RAY DIFFRACTIONf_dihedral_angle_d14.4771653
X-RAY DIFFRACTIONf_chiral_restr0.057710
X-RAY DIFFRACTIONf_plane_restr0.007832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.76760.40391400.34112242X-RAY DIFFRACTION100
2.7676-2.84240.38881430.32632216X-RAY DIFFRACTION100
2.8424-2.9260.35771390.30312228X-RAY DIFFRACTION100
2.926-3.02040.35041430.27522243X-RAY DIFFRACTION100
3.0204-3.12840.30871440.24912235X-RAY DIFFRACTION100
3.1284-3.25360.27651450.22812239X-RAY DIFFRACTION100
3.2536-3.40160.28081410.21892236X-RAY DIFFRACTION100
3.4016-3.58090.26231400.20492259X-RAY DIFFRACTION100
3.5809-3.80510.2261450.16732244X-RAY DIFFRACTION100
3.8051-4.09870.1891450.15582241X-RAY DIFFRACTION100
4.0987-4.51080.1811470.13492254X-RAY DIFFRACTION100
4.5108-5.16270.20221400.13572270X-RAY DIFFRACTION100
5.1627-6.50120.20621380.1682281X-RAY DIFFRACTION100
6.5012-44.32460.20921410.16962340X-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)
10.72030.6709-0.57862.2907-0.88541.4713-0.00630.06730.1179-0.2160.12450.3386-0.3197-0.07860.00010.70630.0026-0.07720.32090.03560.488181.9734-18.8998-25.9207
21.1270.5928-0.46711.75080.18710.8698-0.0850.00560.0235-0.1021-0.1-0.2342-0.37830.1544-0.00090.7511-0.1129-0.06770.3236-0.01350.418393.8485-16.1852-24.686
3-0.18440.4568-0.30680.3316-0.013-0.14080.0107-0.15210.05610.1589-0.2012-0.7307-0.42510.4357-0.00620.8961-0.2272-0.02310.51030.02830.701102.1907-20.7334-24.318
40.3039-0.12270.30790.3954-0.11470.50330.0854-0.1525-0.188-0.0625-0.165-0.3019-0.36830.23390.00010.5628-0.12630.06360.35510.02870.5855100.5405-26.6126-24.8894
50.7535-0.26090.00880.93480.23610.2148-0.0505-0.2755-0.10970.20260.00430.2073-0.0551-0.04720.00040.5534-0.0172-0.01730.54280.03630.499573.8858-39.0378-7.0177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 223 through 492 )
2X-RAY DIFFRACTION2chain 'A' and (resid 493 through 592 )
3X-RAY DIFFRACTION3chain 'A' and (resid 593 through 648 )
4X-RAY DIFFRACTION4chain 'A' and (resid 649 through 749 )
5X-RAY DIFFRACTION5chain 'A' and (resid 750 through 807 )

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