PDB-9fdl: Crystal structure of the catalytic domain of an AA9 lytic polysac...

ID or keywords:

Entry

Database: PDB / ID: 9fdl

Title

Crystal structure of the catalytic domain of an AA9 lytic polysaccharide monooxygenase from Thermothelomyces thermophilus (TtLPMO9F)

Components

Glycoside hydrolase family 61 protein

Keywords

METAL BINDING PROTEIN / LPMO / AA9

Function / homology

Function and homology information

lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose binding / cellulose catabolic process / hydrolase activity / extracellular region / metal ion binding
Similarity search - Function

Biological species

Thermothelomyces thermophilus ATCC 42464 (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.33 Å

Authors

Kosinas, C. / Dimarogona, M. / Topakas, E.

Funding support

Greece, 1items

Citation

Journal: Int.J.Biol.Macromol. / Year: 2024
Title: Mutational study of a lytic polysaccharide monooxygenase from Myceliophthora thermophila (MtLPMO9F): Structural insights into substrate specificity and regioselectivity.
Authors: Kosinas, C. / Chorozian, K. / Sandgren, M. / Topakas, E. / Dimarogona, M.

History

Deposition	May 17, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 25, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9fdl.cif.gz	353.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9fdl.ent.gz	222.3 KB	Display	PDB format
PDBx/mmJSON format	9fdl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fd/9fdl ftp://data.pdbj.org/pub/pdb/validation_reports/fd/9fdl	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycoside hydrolase family 61 protein

B: Glycoside hydrolase family 61 protein

C: Glycoside hydrolase family 61 protein

hetero molecules

73 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycoside hydrolase family 61 protein

hetero molecules

defined by author
Evidence: gel filtration
24.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycoside hydrolase family 61 protein

hetero molecules

defined by author
24.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Glycoside hydrolase family 61 protein

hetero molecules

defined by author
24.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.891, 112.293, 262.381
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-415- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A

NCS domain segments:

Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: SER / End label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Auth seq-ID	Label seq-ID
1	1	1	1 - 229	1 - 229
2	1	1	1 - 229	1 - 229
3	2	2	1 - 227	1 - 227
4	2	2	1 - 227	1 - 227
5	3	3	1 - 227	1 - 227
6	3	3	1 - 227	1 - 227

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

-
Protein , 1 types, 3 molecules ABC

#1: Protein	Glycoside hydrolase family 61 protein Mass: 24149.842 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Prior to crystallisation, the full length protein (UniProt ID G2Q9F7) was submitted to treatment with papain, to remove the carbohydrate binding module, appended at the protein C-terminal. ...Details: Prior to crystallisation, the full length protein (UniProt ID G2Q9F7) was submitted to treatment with papain, to remove the carbohydrate binding module, appended at the protein C-terminal. The catalytic domain was purified and crystallised. Source: (gene. exp.) Thermothelomyces thermophilus ATCC 42464 (fungus) Gene: MYCTH_111088 / Production host: Komagataella pastoris (fungus) / References: UniProt: G2Q9F7

#1: Protein

Glycoside hydrolase family 61 protein

Mass: 24149.842 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Prior to crystallisation, the full length protein (UniProt ID G2Q9F7) was submitted to treatment with papain, to remove the carbohydrate binding module, appended at the protein C-terminal. ...
Source: (gene. exp.)

Thermothelomyces thermophilus ATCC 42464 (fungus)
Gene: MYCTH_111088 / Production host:

Komagataella pastoris (fungus) / References: UniProt: G2Q9F7

-
Non-polymers , 6 types, 348 molecules

#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#6: Chemical	ChemComp-CU / COPPER (II) ION Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M of sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.33→262.38 Å / Num. obs: 35897 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.993 / R_merge(I) obs: 0.324 / R_pim(I) all: 0.132 / R_rim(I) all: 0.35 / Net I/σ(I): 6.5
Reflection shell	Resolution: 2.33→2.41 Å / Redundancy: 14.1 % / R_merge(I) obs: 2.476 / Num. unique obs: 48717 / CC_1/2: 0.534 / R_pim(I) all: 0.681 / R_rim(I) all: 2.569

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
REFMAC	5.8.0419	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.33→131.536 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.947 / SU B: 13.243 / SU ML: 0.157 / Cross valid method: FREE R-VALUE / ESU R: 0.259 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions. TLS added.

	R_factor	Num. reflection	% reflection
R_free	0.2041	1755	4.898 %
R_work	0.1623	34073	-
all	0.164	-	-
obs	-	35828	99.922 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 44.215 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.215 Å²	0 Å²	-0 Å²
2-	-	-0.786 Å²	0 Å²
3-	-	-	1.001 Å²

Refinement step

Cycle: LAST / Resolution: 2.33→131.536 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5085	0	30	341	5456

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	5280
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4781
X-RAY DIFFRACTION	r_angle_refined_deg	1.857	1.759	7194
X-RAY DIFFRACTION	r_angle_other_deg	0.627	1.73	11010
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.485	5	687
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.454	5	21
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.004	10	727
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.689	10	232
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	751
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	6471
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1233
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	916
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	4750
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	2648
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	2960
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	278
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.035	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.114	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.181	0.2	96
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.099	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	3.329	3.2	2751
X-RAY DIFFRACTION	r_mcbond_other	3.329	3.2	2751
X-RAY DIFFRACTION	r_mcangle_it	4.544	5.736	3437
X-RAY DIFFRACTION	r_mcangle_other	4.544	5.736	3438
X-RAY DIFFRACTION	r_scbond_it	4.173	3.502	2529
X-RAY DIFFRACTION	r_scbond_other	4.172	3.503	2530
X-RAY DIFFRACTION	r_scangle_it	5.92	6.248	3757
X-RAY DIFFRACTION	r_scangle_other	5.92	6.249	3758
X-RAY DIFFRACTION	r_lrange_it	7.524	30.419	5679
X-RAY DIFFRACTION	r_lrange_other	7.446	30.308	5628
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.08	0.05	7115
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.087	0.05	7009
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.085	0.05	7004

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08015	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08015	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08736	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08736	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.08471	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.08471	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.33-2.391	0.315	113	0.265	2470	0.267	2584	0.928	0.952	99.9613	0.27
2.391-2.456	0.3	107	0.251	2424	0.253	2533	0.938	0.954	99.921	0.255
2.456-2.527	0.272	121	0.228	2374	0.23	2496	0.939	0.963	99.9599	0.23
2.527-2.605	0.273	144	0.22	2284	0.224	2430	0.943	0.966	99.9177	0.22
2.605-2.69	0.253	107	0.193	2222	0.196	2332	0.959	0.976	99.8714	0.191
2.69-2.785	0.207	96	0.182	2163	0.183	2261	0.973	0.98	99.9115	0.178
2.785-2.89	0.221	109	0.168	2076	0.17	2187	0.969	0.983	99.9085	0.161
2.89-3.008	0.226	127	0.161	1967	0.165	2095	0.966	0.984	99.9523	0.152
3.008-3.141	0.2	85	0.153	1973	0.155	2059	0.971	0.985	99.9514	0.144
3.141-3.295	0.185	91	0.149	1854	0.151	1946	0.979	0.986	99.9486	0.14
3.295-3.473	0.147	91	0.125	1759	0.126	1850	0.986	0.991	100	0.119
3.473-3.683	0.184	73	0.133	1682	0.135	1755	0.981	0.989	100	0.128
3.683-3.937	0.185	82	0.139	1554	0.141	1638	0.982	0.989	99.8779	0.135
3.937-4.252	0.179	90	0.13	1450	0.133	1542	0.98	0.99	99.8703	0.129
4.252-4.658	0.163	66	0.128	1373	0.13	1440	0.987	0.99	99.9306	0.129
4.658-5.207	0.179	75	0.137	1230	0.139	1306	0.982	0.989	99.9234	0.141
5.207-6.011	0.226	52	0.164	1094	0.167	1146	0.981	0.986	100	0.167
6.011-7.358	0.182	49	0.171	942	0.171	991	0.981	0.982	100	0.174
7.358-10.389	0.219	51	0.169	746	0.172	797	0.967	0.982	100	0.176
10.389-131.536	0.241	26	0.259	436	0.258	468	0.975	0.949	98.7179	0.281

Refinement TLS params.

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

ID	L11 (°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)
1	1.4594	0.1525	0.9482	1.3597	0.6244	3.1717	-0.0114	0.1506	0.0629	-0.0893	-0.0032	0.0089	-0.1146	0.1671	0.0146	0.0111	0.0001	0.0052	0.0203	0.0096	0.0114	-13.3726	-17.4523	-8.4995
2	1.6574	0.0594	1.0464	1.4176	0.8431	3.3311	0.011	0.1236	-0.1384	-0.1117	-0.0156	0.0761	0.1006	0.1492	0.0046	0.076	0.0375	-0.0151	0.0622	-0.0358	0.1242	-9.8762	-47.2927	-26.0567
3	1.8395	0.3084	0.4857	1.8414	0.2419	3.2635	-0.0573	0.1182	-0.0195	-0.1171	0.0167	0.1705	-0.0305	-0.0465	0.0406	0.1201	0.0619	-0.0553	0.1339	-0.027	0.051	-30.0657	-21.4642	-48.318

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 6 types, 348 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 3 molecules ABC

-Non-polymers , 6 types, 348 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 6 types, 348 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi