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- PDB-5nlt: CvAA9A -

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Basic information

Entry
Database: PDB / ID: 5nlt
TitleCvAA9A
ComponentsCvAA9A
KeywordsOXIDOREDUCTASE / Enzyme
Function / homology
Function and homology information


cellulase / monooxygenase activity / hydrolase activity / extracellular region
Similarity search - Function
Coagulation Factor XIII; Chain A, domain 1 - #70 / Auxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesCollariella virescens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFrandsen, K.E.H. / Poulsen, J.-C.N. / Tandrup, T. / Schnorr, K. / Tovborg, M. / Lo Leggio, L.
Funding support Denmark, 1items
OrganizationGrant numberCountry
The Danish Council for Strategic Research12-134923 Denmark
CitationJournal: Nat Commun / Year: 2017
Title: Structural and electronic determinants of lytic polysaccharide monooxygenase reactivity on polysaccharide substrates.
Authors: Simmons, T.J. / Frandsen, K.E.H. / Ciano, L. / Tryfona, T. / Lenfant, N. / Poulsen, J.C. / Wilson, L.F.L. / Tandrup, T. / Tovborg, M. / Schnorr, K. / Johansen, K.S. / Henrissat, B. / Walton, ...Authors: Simmons, T.J. / Frandsen, K.E.H. / Ciano, L. / Tryfona, T. / Lenfant, N. / Poulsen, J.C. / Wilson, L.F.L. / Tandrup, T. / Tovborg, M. / Schnorr, K. / Johansen, K.S. / Henrissat, B. / Walton, P.H. / Lo Leggio, L. / Dupree, P.
History
DepositionApr 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn_type.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CvAA9A
B: CvAA9A
C: CvAA9A
D: CvAA9A
E: CvAA9A
F: CvAA9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,89720
Polymers166,7476
Non-polymers1,15014
Water18,5731031
1
A: CvAA9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8552
Polymers27,7911
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CvAA9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7911
Non-polymers1602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CvAA9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8552
Polymers27,7911
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CvAA9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0474
Polymers27,7911
Non-polymers2563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: CvAA9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1435
Polymers27,7911
Non-polymers3524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: CvAA9A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0474
Polymers27,7911
Non-polymers2563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.000, 59.420, 115.450
Angle α, β, γ (deg.)102.67, 98.89, 89.54
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: HIC / Beg label comp-ID: HIC / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA1 - 2231 - 223
21ASPASPBB1 - 2231 - 223
12ASPASPAA1 - 2231 - 223
22ASPASPCC1 - 2231 - 223
13ALAALAAA1 - 2241 - 224
23ALAALADD1 - 2241 - 224
14ASPASPAA1 - 2231 - 223
24ASPASPEE1 - 2231 - 223
15ALAALAAA1 - 2241 - 224
25ALAALAFF1 - 2241 - 224
16GLNGLNBB1 - 2251 - 225
26GLNGLNCC1 - 2251 - 225
17ASPASPBB1 - 2231 - 223
27ASPASPDD1 - 2231 - 223
18GLNGLNBB1 - 2251 - 225
28GLNGLNEE1 - 2251 - 225
19ASPASPBB1 - 2231 - 223
29ASPASPFF1 - 2231 - 223
110ASPASPCC1 - 2231 - 223
210ASPASPDD1 - 2231 - 223
111ASPASPCC1 - 2261 - 226
211ASPASPEE1 - 2261 - 226
112ASPASPCC1 - 2231 - 223
212ASPASPFF1 - 2231 - 223
113ASPASPDD1 - 2231 - 223
213ASPASPEE1 - 2231 - 223
114ALAALADD1 - 2241 - 224
214ALAALAFF1 - 2241 - 224
115ASPASPEE1 - 2231 - 223
215ASPASPFF1 - 2231 - 223

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
CvAA9A


Mass: 27791.133 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Collariella virescens / Source: (gene. exp.) Collariella virescens (fungus) / Production host: Aspergillus oryzae (mold) / Variant (production host): MT3568 / References: UniProt: A0A223GEC9*PLUS, Oxidoreductases
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1031 / 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 % sol: 33.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.6 M (NH4)2SO4 0.1M NaCl 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 90992 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 2.16 % / CC1/2: 0.991 / Rrim(I) all: 0.124 / Net I/σ(I): 6.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 1.69 % / Mean I/σ(I) obs: 1.22 / Num. unique obs: 6493 / CC1/2: 0.643 / Rrim(I) all: 0.828 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ACH

5ach


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.044 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.187 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24441 4376 5.1 %RANDOM
Rwork0.19792 ---
obs0.20034 80720 89.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.378 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20.99 Å20.79 Å2
2--0.43 Å2-0.26 Å2
3----1.57 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10532 0 46 1031 11609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211091
X-RAY DIFFRACTIONr_bond_other_d0.0110.029890
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.94915157
X-RAY DIFFRACTIONr_angle_other_deg1.847322965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84851386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17924.812505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.434151631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9171538
X-RAY DIFFRACTIONr_chiral_restr0.1010.21551
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112746
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022506
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_it2.112.5025466
X-RAY DIFFRACTIONr_mcbond_other2.1092.5015465
X-RAY DIFFRACTIONr_mcangle_it3.2023.7456839
X-RAY DIFFRACTIONr_mcangle_other3.2013.7466840
X-RAY DIFFRACTIONr_scbond_it2.5932.7035625
X-RAY DIFFRACTIONr_scbond_other2.5322.6785594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.953.9138258
X-RAY DIFFRACTIONr_long_range_B_refined6.17620.65613477
X-RAY DIFFRACTIONr_long_range_B_other6.08120.46813056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A259400.08
12B259400.08
21A257720.09
22C257720.09
31A260860.09
32D260860.09
41A261020.08
42E261020.08
51A259700.09
52F259700.09
61B254940.1
62C254940.1
71B257300.07
72D257300.07
81B260160.09
82E260160.09
91B256000.08
92F256000.08
101C258560.08
102D258560.08
111C259020.09
112E259020.09
121C256080.09
122F256080.09
131D259800.08
132E259800.08
141D259420.08
142F259420.08
151E259980.09
152F259980.09
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 197 -
Rwork0.42 3627 -
obs--54.57 %

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