PDB-9i4f: Blood Type B-converting alpha-1,3-galactosidase PpaGal from Pedob...

ID or keywords:

Entry

Database: PDB / ID: 9i4f

Title

Blood Type B-converting alpha-1,3-galactosidase PpaGal from Pedobacter panaciterrae in its apo form

Components

Alpha-1,3-galactosidase PpaGal

Keywords

HYDROLASE / alpha-1 / 3-galactopyranosidase / galactosidase / D-galactose / blood conversion / B-antigen removal / beta-helix / beta-barrel

Biological species

Pedobacter panaciterrae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Schmoeker, O. / Moeller, C. / Terholsen, H. / Girbardt, B. / Palm, G.J. / Hoppen, J. / Lammers, M. / Bornscheuer, U.T.

Funding support

Germany, 1items

Citation

Journal: Chembiochem / Year: 2025
Title: Identification and Protein Engineering of Galactosidases for the Conversion of Blood Type B to Blood Type O.
Authors: Moller, C. / Terholsen, H. / Schmoker, O. / Le, T.L.A. / Wesche, J. / Schmiade, P. / Eppendorfer, E. / Rimkus, N. / Girbardt, B. / Bottcher, D. / Palm, G.J. / Hoppen, J. / Lammers, M. / ...

History

Deposition	Jan 24, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 12, 2025	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2025	Group: Database references / Category: citation Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Apr 30, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9i4f.cif.gz	1.5 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	9i4f_validation.pdf.gz	472.7 KB	Display	wwPDB validaton report
Full document	9i4f_full_validation.pdf.gz	499.1 KB	Display
Data in XML	9i4f_validation.xml.gz	88.7 KB	Display
Data in CIF	9i4f_validation.cif.gz	114 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i4/9i4f ftp://data.pdbj.org/pub/pdb/validation_reports/i4/9i4f	HTTPS FTP

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Related structure data

Related structure data	9i4gC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Alpha-1,3-galactosidase PpaGal

B: Alpha-1,3-galactosidase PpaGal

C: Alpha-1,3-galactosidase PpaGal

D: Alpha-1,3-galactosidase PpaGal

hetero molecules

263 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Alpha-1,3-galactosidase PpaGal

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

2

B: Alpha-1,3-galactosidase PpaGal

hetero molecules

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

3

C: Alpha-1,3-galactosidase PpaGal

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

4

D: Alpha-1,3-galactosidase PpaGal

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

Unit cell

Length a, b, c (Å)	107.130, 129.026, 108.296
Angle α, β, γ (deg.)	90.000, 90.177, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
3	2	B
4	2	D
5	3	B
6	3	C
7	4	A
8	4	D
9	5	A
10	5	C
11	6	D
12	6	C

NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 34 - 617 / Label seq-ID: 1 - 584

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	B	B
2	2	1	A	A
3	3	2	B	B
4	4	2	D	D
5	5	3	B	B
6	6	3	C	C
7	7	4	A	A
8	8	4	D	D
9	9	5	A	A
10	10	5	C	C
11	11	6	D	D
12	12	6	C	C

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
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Alpha-1,3-galactosidase PpaGal Mass: 65858.797 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Starting amino acids SEF correspond to EcoRI restriction site from molecular cloning, N37 corresponds to N20 in Pedobacter PpaGal (GenBank: NQX53349.1). Source: (gene. exp.) Pedobacter panaciterrae (bacteria) / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: alpha-galactosidase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 0.2 M lithium citrate, 20% PEG 3350

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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: 0.97626 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2024

Radiation

Monochromator: SILICON111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97626 Å / Relative weight: 1

Reflection

Resolution: 2.75→107.13 Å / Num. obs: 73785 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 30.94 Å² / CC_1/2: 0.994 / R_pim(I) all: 0.094 / R_rim(I) all: 0.192 / R_sym value: 0.167 / Net I/σ(I): 6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	R_sym value	% possible all
2.75-2.797	3.6	2	3796	0.865	0.407	0.785	0.669	100
7.462-107.13	3.9	13.4	3902	0.998	0.03	0.06	0.052	98.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Coot	0.9.8.95	model building
PHASER	2.8.3	phasing
XDS	BUILT 20230630	data scaling
XDS	BUILT 20230630	data reduction
MxCuBE		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→107.13 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.903 / SU B: 42.686 / SU ML: 0.364 / Cross valid method: FREE R-VALUE / ESU R Free: 0.417
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2854	3647	4.954 %
R_work	0.251	69967	-
all	0.253	-	-
obs	-	73614	96.175 %

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: 34.812 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.746 Å²	-0 Å²	-0.444 Å²
2-	-	1.604 Å²	0 Å²
3-	-	-	0.144 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→107.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18556	0	4	63	18623

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	18987
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	17993
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.279	0.1	324100
X-RAY DIFFRACTION	r_angle_refined_deg	1.96	1.644	25674
X-RAY DIFFRACTION	r_angle_other_deg	1.46	1.585	41571
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.688	5	2332
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.308	23.691	932
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.645	15	3376
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.835	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2552
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	21456
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4336
X-RAY DIFFRACTION	r_nbd_refined	0.198	0.2	3157
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.202	0.2	16893
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	8899
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	10782
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	324
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.001	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.207	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.223	0.2	140
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.246	0.2	13
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.027	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	0.984	1.843	9340
X-RAY DIFFRACTION	r_mcbond_other	0.983	1.843	9339
X-RAY DIFFRACTION	r_mcangle_it	1.706	2.762	11668
X-RAY DIFFRACTION	r_mcangle_other	1.706	2.762	11669
X-RAY DIFFRACTION	r_scbond_it	1.04	1.967	9647
X-RAY DIFFRACTION	r_scbond_other	1.04	1.967	9647
X-RAY DIFFRACTION	r_scangle_it	1.824	2.896	14006
X-RAY DIFFRACTION	r_scangle_other	1.824	2.896	14006
X-RAY DIFFRACTION	r_lrange_it	4.902	67.622	332994
X-RAY DIFFRACTION	r_lrange_other	4.901	67.622	332987
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.062	0.05	19658
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.059	0.05	19671
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.064	0.05	19592
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.064	0.05	19641
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.065	0.05	19608
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.067	0.05	19617

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	B	X-RAY DIFFRACTION	Local ncs	0.06177	0.05011
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06177	0.05011
2	3	B	X-RAY DIFFRACTION	Local ncs	0.05894	0.05011
2	4	D	X-RAY DIFFRACTION	Local ncs	0.05894	0.05011
3	5	B	X-RAY DIFFRACTION	Local ncs	0.06431	0.05011
3	6	C	X-RAY DIFFRACTION	Local ncs	0.06431	0.05011
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06385	0.05011
4	8	D	X-RAY DIFFRACTION	Local ncs	0.06385	0.05011
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06499	0.05011
5	10	C	X-RAY DIFFRACTION	Local ncs	0.06499	0.05011
6	11	D	X-RAY DIFFRACTION	Local ncs	0.06679	0.05011
6	12	C	X-RAY DIFFRACTION	Local ncs	0.06679	0.05011

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.75-2.821	0.375	245	0.386	5354	X-RAY DIFFRACTION	99.9286
2.821-2.899	0.386	301	0.349	5195	X-RAY DIFFRACTION	99.7821
2.899-2.983	0.398	289	0.336	5032	X-RAY DIFFRACTION	99.8311
2.983-3.074	0.356	216	0.31	4992	X-RAY DIFFRACTION	99.8466
3.074-3.175	0.338	267	0.292	4754	X-RAY DIFFRACTION	99.7418
3.175-3.287	0.264	282	0.271	4559	X-RAY DIFFRACTION	99.7939
3.287-3.411	0.298	247	0.269	4437	X-RAY DIFFRACTION	99.7232
3.411-3.55	0.347	242	0.332	4040	X-RAY DIFFRACTION	94.588
3.55-3.707	0.255	187	0.235	3051	X-RAY DIFFRACTION	74.249
3.707-3.888	0.251	143	0.235	3224	X-RAY DIFFRACTION	81.0934
3.888-4.098	0.247	163	0.208	3177	X-RAY DIFFRACTION	84.4714
4.098-4.347	0.221	164	0.192	3586	X-RAY DIFFRACTION	99.8137
4.347-4.646	0.189	129	0.166	3389	X-RAY DIFFRACTION	99.7166
4.646-5.018	0.221	141	0.168	3092	X-RAY DIFFRACTION	99.5688
5.018-5.496	0.245	166	0.19	2852	X-RAY DIFFRACTION	99.9669
5.496-6.144	0.225	116	0.193	2628	X-RAY DIFFRACTION	99.8181
6.144-7.091	0.267	123	0.212	2305	X-RAY DIFFRACTION	99.7535
7.091-8.679	0.268	122	0.208	1926	X-RAY DIFFRACTION	99.8051
8.679-12.246	0.244	75	0.203	1523	X-RAY DIFFRACTION	99.5639
12.246-107.13	0.265	29	0.337	851	X-RAY DIFFRACTION	95.8606

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	0.4109	-0.1768	0.0349	0.0897	-0.0078	0.4316	-0.0265	0.0212	0.0098	-0.0069	0.0306	0.0102	-0.0385	0.0638	-0.0041	0.0372	0.0026	-0.0267	0.5133	-0.0082	0.022	23.9714	13.7274	21.7585
2	0.3681	0.1429	-0.0175	0.0578	-0.0091	0.4393	-0.0008	0.0103	0.0083	0.0066	0.0294	-0.0006	-0.0352	-0.0084	-0.0287	0.0408	-0.0005	-0.0265	0.546	0.012	0.0235	71.5196	13.9948	-11.5589
3	0.5372	0.1959	-0.059	0.0782	-0.0162	0.3893	0.0013	-0.033	-0.008	-0.0135	0.0083	0.0089	0.0183	0.0503	-0.0096	0.0384	0.0231	-0.031	0.5083	-0.0054	0.0255	77.4316	-2.7475	42.5972
4	0.4276	0.2261	-0.0026	0.1264	-0.0008	0.4464	0.0127	-0.0304	-0.0079	-0.0062	0.0107	0.007	0.0291	0.0403	-0.0233	0.0407	0.018	-0.0315	0.4969	-0.0008	0.0247	89.0769	61.8256	32.3306

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	B	34 - 617
2	X-RAY DIFFRACTION	2	ALL	A	34 - 617
3	X-RAY DIFFRACTION	3	ALL	D	34 - 617
4	X-RAY DIFFRACTION	4	ALL	C	34 - 617

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