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- PDB-5ufv: Crystal Structure of a Cellulose-active Polysaccharide Monooxygen... -

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Basic information

Entry
Database: PDB / ID: 5ufv
TitleCrystal Structure of a Cellulose-active Polysaccharide Monooxygenase from M. thermophila (MtPMO3*)
ComponentsGlycoside hydrolase family 61 protein
KeywordsHydrolase/OXIDOREDUCTASE / Copper proteins / Oxygen / Fungal proteins / Biocatalysis / Oxidation-Reduction / Hydrolase-OXIDOREDUCTASE complex
Function / homology
Function and homology information


hydrolase activity / extracellular region / metal ion binding
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 / Glycoside hydrolase family 61 protein
Similarity search - Component
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSpan, E.A. / Deller, M.C. / Marletta, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Energy Biosciences Institute022711 United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: The Role of the Secondary Coordination Sphere in a Fungal Polysaccharide Monooxygenase.
Authors: Span, E.A. / Suess, D.L.M. / Deller, M.C. / Britt, R.D. / Marletta, M.A.
History
DepositionJan 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: 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: Glycoside hydrolase family 61 protein
B: Glycoside hydrolase family 61 protein
C: Glycoside hydrolase family 61 protein
D: Glycoside hydrolase family 61 protein
E: Glycoside hydrolase family 61 protein
F: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,75212
Polymers152,3706
Non-polymers3816
Water5,314295
1
A: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4592
Polymers25,3951
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4592
Polymers25,3951
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4592
Polymers25,3951
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4592
Polymers25,3951
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4592
Polymers25,3951
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glycoside hydrolase family 61 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4592
Polymers25,3951
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.937, 134.302, 79.402
Angle α, β, γ (deg.)90.000, 92.920, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIC / Beg label comp-ID: HIC / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4 / Auth seq-ID: 1 - 228 / Label seq-ID: 1 - 228

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999981, 0.002231, -0.005684), (-0.001878, -0.998111, -0.061414), (-0.00581, -0.061402, 0.998096)123.729622, 96.395447, 3.46145
3given(0.203696, -0.628624, -0.750559), (0.574216, 0.697637, -0.428462), (0.792959, -0.343707, 0.503072)50.86433, 45.534679, -36.938599
4given(-0.199567, 0.555324, 0.807334), (0.781281, -0.407099, 0.47315), (0.591417, 0.725179, -0.35262)60.197929, 18.703251, -16.54344
5given(0.169741, 0.593623, 0.786638), (0.589495, -0.700828, 0.401666), (0.789736, 0.39554, -0.468898)-20.97295, 39.27998, 1.65841
6given(-0.170715, -0.541317, -0.823306), (0.75343, 0.46676, -0.463118), (0.63498, -0.699365, 0.328161)69.956947, 20.63604, 12.18583

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Components

#1: Protein
Glycoside hydrolase family 61 protein


Mass: 25395.045 Da / Num. of mol.: 6 / Fragment: UNP residues 18-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_92668 / Plasmid: pCSR1 / Production host: Neurospora crassa (fungus) / References: UniProt: G2QAB5
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 3.9 / Details: 18% PEG 6K, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 53718 / % possible obs: 98.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.139 / Net I/av σ(I): 9.604 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured obsDiffraction-ID% possible all
2.45-2.544.20.55288197.1
2.54-2.644.70.424199
2.64-2.764.70.353199
2.76-2.94.70.268199
2.9-3.094.60.215199.1
3.09-3.324.40.159197.1
3.32-3.664.80.138199.2
3.66-4.194.70.115199.3
4.19-5.284.50.097197.7
5.28-504.60.086198.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VTC

2vtc


Resolution: 2.45→48.74 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 19.171 / SU ML: 0.187 / SU R Cruickshank DPI: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.461 / ESU R Free: 0.238
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 2726 5.1 %RANDOM
Rwork0.162 ---
obs0.1643 50966 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.95 Å2 / Biso mean: 36.512 Å2 / Biso min: 16.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å2-2.04 Å2
2--1.97 Å2-0 Å2
3----1.83 Å2
Refinement stepCycle: final / Resolution: 2.45→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10344 0 6 295 10645
Biso mean--35.32 31.64 -
Num. residues----1368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910770
X-RAY DIFFRACTIONr_bond_other_d0.0020.029436
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.93214732
X-RAY DIFFRACTIONr_angle_other_deg0.773321890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24251370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14925.217460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65151432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3541512
X-RAY DIFFRACTIONr_chiral_restr0.0730.21492
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112544
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022486
X-RAY DIFFRACTIONr_mcbond_it1.4742.855474
X-RAY DIFFRACTIONr_mcbond_other1.4742.8495473
X-RAY DIFFRACTIONr_mcangle_it2.3674.276834
Refine LS restraints NCS

Ens-ID: 1 / Number: 3264 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.410.5
2BMEDIUM POSITIONAL0.30.5
3CMEDIUM POSITIONAL0.340.5
4DMEDIUM POSITIONAL0.440.5
5EMEDIUM POSITIONAL0.310.5
6FMEDIUM POSITIONAL0.390.5
1AMEDIUM THERMAL3.542
2BMEDIUM THERMAL2.952
3CMEDIUM THERMAL3.592
4DMEDIUM THERMAL3.532
5EMEDIUM THERMAL3.022
6FMEDIUM THERMAL3.292
LS refinement shellResolution: 2.449→2.512 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 194 -
Rwork0.249 3585 -
all-3779 -
obs--94.74 %
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)
11.6912-0.0457-0.5250.8109-0.05671.2527-0.01130.08150.22910.03520.0212-0.0739-0.07730.0422-0.00990.0089-0.0073-0.01560.01370.02450.069941.40861.08225.793
21.43440.10160.57810.75140.45791.35370.09810.0261-0.12460.1-0.040.02270.1243-0.0408-0.05810.0247-0.0088-0.0160.0196-0.00810.049682.26433.68524.922
30.68040.19660.19840.91390.08021.3176-0.05760.08220.0703-0.06360.0733-0.0242-0.0430.1412-0.01570.0193-0.01340.00320.0360.01030.019256.774-4.76132.019
41.26940.31-0.56570.7768-0.28991.27650.0195-0.120.07840.0024-0.0143-0.0115-0.03780.1274-0.00530.02970.0093-0.01750.0503-0.02250.020461.9053.005-10.039
51.0411-0.0108-0.12570.53030.02130.82010.1068-0.107-0.13510.0431-0.0326-0.05160.05390.026-0.07420.0621-0.0236-0.05290.02480.02560.051342.51231.29946.509
60.46950.15010.45611.0534-0.11921.7389-0.03370.0775-0.07910.05140.1455-0.0702-0.07980.0125-0.11180.01490.01710.0020.0923-0.04750.03644.00224.8019.24
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 228
2X-RAY DIFFRACTION2B1 - 228
3X-RAY DIFFRACTION3C1 - 228
4X-RAY DIFFRACTION4D1 - 228
5X-RAY DIFFRACTION5E1 - 228
6X-RAY DIFFRACTION6F1 - 228

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