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- PDB-5nz8: Clostridium thermocellum cellodextrin phosphorylase with cellotet... -

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Basic information

Entry
Database: PDB / ID: 5nz8
TitleClostridium thermocellum cellodextrin phosphorylase with cellotetraose and phosphate bound
ComponentsCellodextrin phosphorylase
KeywordsHYDROLASE / glycoside hydrolase family 94 / cellodextrin phosphorylase / cellulose synthesis
Function / homology
Function and homology information


glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose mutarotase-like domain superfamily
Similarity search - Domain/homology
beta-cellotetraose / PHOSPHATE ION / Cellodextrin phosphorylase
Similarity search - Component
Biological speciesClostridium thermocellum (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsO'Neill, E.C. / Pergolizzi, G. / Stevenson, C.E.M. / Lawson, D.M. / Nepogodiev, S.A. / Field, R.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 (MET) United Kingdom
EPSRC and InnovateUKBB/M02903411 United Kingdom
John Innes Foundation United Kingdom
CitationJournal: Carbohydr. Res. / Year: 2017
Title: Cellodextrin phosphorylase from Ruminiclostridium thermocellum: X-ray crystal structure and substrate specificity analysis.
Authors: O'Neill, E.C. / Pergolizzi, G. / Stevenson, C.E.M. / Lawson, D.M. / Nepogodiev, S.A. / Field, R.A.
History
DepositionMay 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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: Cellodextrin phosphorylase
B: Cellodextrin phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,5186
Polymers228,9952
Non-polymers1,5234
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-26 kcal/mol
Surface area63100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.810, 152.970, 92.220
Angle α, β, γ (deg.)90.000, 114.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 984
2010B1 - 984

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Components

#1: Protein Cellodextrin phosphorylase /


Mass: 114497.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was expressed with a 25 residue nickel affinity tag with sequence MGSSHHHHHHSSGLVPRGSHMLEDP appended to the N-terminus of the full-length amino acid sequence
Source: (gene. exp.) Clostridium thermocellum (unknown) / Gene: cdp-ym4 / Production host: Escherichia coli BL21(DE3) (unknown) / Strain (production host): Star / References: UniProt: Q93HT8
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→27.62 Å / Num. obs: 41938 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.041 / Rrim(I) all: 0.077 / Net I/σ(I): 12.8 / Num. measured all: 141679 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.083.41.0860.4250.6921.29194.8
13.42-27.623.20.0210.9990.0140.02580

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
REFMAC5refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMAC5phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5NZ7
Resolution: 3→27.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 58.237 / SU ML: 0.449 / SU R Cruickshank DPI: 0.4498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.487
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 2133 5.2 %RANDOM
Rwork0.2101 ---
obs0.2128 39167 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 213.65 Å2 / Biso mean: 106.195 Å2 / Biso min: 67.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.47 Å20 Å20.03 Å2
2---4.06 Å20 Å2
3---4.6 Å2
Refinement stepCycle: final / Resolution: 3→27.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14027 0 100 0 14127
Biso mean--133.71 --
Num. residues----1858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914451
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212578
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.93819676
X-RAY DIFFRACTIONr_angle_other_deg0.899328896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20951848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36724.094640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.367152060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3931564
X-RAY DIFFRACTIONr_chiral_restr0.0660.22244
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023140
Refine LS restraints NCS

Ens-ID: 1 / Number: 53420 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.001→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 134 -
Rwork0.35 2438 -
all-2572 -
obs--82.65 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.59670.40691.51341.5791-1.45515.8426-0.1771-0.39470.42190.3136-0.0074-0.3892-0.33390.51330.18450.12230.0316-0.09350.5916-0.22120.547623.0145-11.599842.0915
23.0382-1.5307-0.22351.68850.51761.8001-0.1448-0.4996-0.46980.33110.27550.45930.2687-0.0046-0.13070.1235-0.0031-0.01160.15290.20830.3985-11.252-34.514143.1541
31.70770.2273-1.16740.37340.67353.3635-0.16881.22610.1096-0.14830.23830.210.4073-0.6734-0.06950.696-0.127-0.49990.9020.15510.7667-1.9601-49.388515.7414
43.149-0.4872-0.86192.59210.21681.3575-0.00250.3674-0.1514-0.60640.1728-0.11380.28760.2881-0.17030.3460.119-0.12830.3148-0.04490.329517.2618-46.398418.0709
52.0725-0.9235-1.05713.44793.21794.3122-0.2325-0.879-0.08540.77660.09130.3198-0.0002-0.15350.14120.59380.1930.09620.66190.24110.5873-33.6529-15.08857.5614
63.3552-1.1960.13422.00680.14851.4715-0.0067-0.10370.71830.03650.1276-0.2791-0.18290.2584-0.12090.0398-0.049-0.0350.07560.01320.3818-6.66310.24931.1253
70.08770.00940.12570.60581.38334.05630.08090.2495-0.0677-0.30220.02750.03870.0915-0.0542-0.10840.8432-0.116-0.10250.9910.15210.9987-31.4851-4.87872.0707
83.54470.2641-0.36872.5235-0.91442.3084-0.06550.50480.1028-0.48660.25090.54170.0474-0.4307-0.18530.1053-0.0251-0.12060.24980.2080.5044-44.3880.032619.971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 118
2X-RAY DIFFRACTION2A119 - 481
3X-RAY DIFFRACTION3A482 - 694
4X-RAY DIFFRACTION4A695 - 984
5X-RAY DIFFRACTION5B1 - 104
6X-RAY DIFFRACTION6B105 - 479
7X-RAY DIFFRACTION7B480 - 704
8X-RAY DIFFRACTION8B705 - 984

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