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- PDB-2yox: Bacillus amyloliquefaciens CBM33 in complex with Cu(I) after phot... -

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Basic information

Entry
Database: PDB / ID: 2yox
TitleBacillus amyloliquefaciens CBM33 in complex with Cu(I) after photoreduction
ComponentsRBAM17540
KeywordsOXIDOREDUCTASE / CELLULOSE OXIDATION / GH61 / CELLULOSE DEGRADATION
Function / homologychitin-binding protein cbp21 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / COPPER (I) ION / :
Function and homology information
Biological speciesBACILLUS AMYLOLIQUEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHemsworth, G.R. / Taylor, E.J. / Kim, R.Q. / Lewis, S.J. / Turkenburg, J.P. / Davies, G.J. / Walton, P.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: The Copper Active Site of Cbm33 Polysaccharide Oxygenases.
Authors: Hemsworth, G.R. / Taylor, E.J. / Kim, R.Q. / Gregory, R.C. / Lewis, S.J. / Turkenburg, J.P. / Parkin, A. / Davies, G.J. / Walton, P.H.
History
DepositionOct 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: RBAM17540
B: RBAM17540
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5634
Polymers39,4362
Non-polymers1272
Water3,909217
1
A: RBAM17540
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7812
Polymers19,7181
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RBAM17540
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7812
Polymers19,7181
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.765, 73.549, 75.846
Angle α, β, γ (deg.)90.00, 100.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 28 - 205 / Label seq-ID: 1 - 178

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.85017, -0.01721, 0.52623), (0.017, -0.99984, -0.00523), (0.52624, 0.0045, 0.85033)
Vector: -10.35978, 31.97451, -37.38125)

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Components

#1: Protein RBAM17540 / CBM33 COPPER OXIDASE


Mass: 19717.844 Da / Num. of mol.: 2 / Fragment: RESIDUES 28-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS AMYLOLIQUEFACIENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E1UUV3, Oxidoreductases
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLEADER PEPTIDE WAS NOT INCLUDED IN THE CONSTRUCT BUT REPLACED BY PELB LEADER TO DIRECT PROTEIN TO PERIPLASM

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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: 2.18 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 4 / Details: 0.1 M MMT BUFFER PH 4.0, 25% PEG-1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2012 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.9→19.93 Å / Num. obs: 29332 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BEN

2ben


Resolution: 1.9→19.93 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.868 / SU B: 4.375 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26964 1481 5.1 %RANDOM
Rwork0.21506 ---
obs0.21782 27833 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: SIMPLE MODEL WITH MASK
Displacement parametersBiso mean: 15.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å2-0.91 Å2
2---0.13 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 2 217 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192872
X-RAY DIFFRACTIONr_bond_other_d0.0040.022582
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9053916
X-RAY DIFFRACTIONr_angle_other_deg0.95235938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7755354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39224.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33915420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0411510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213342
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02716
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10383 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 111 -
Rwork0.278 2080 -
obs--98.92 %

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