PDB-9gv3: Crystal structure of the complex between Nb474 mutant R53A,D125A ...

ID or keywords:

Entry

Database: PDB / ID: 9gv3

Title

Crystal structure of the complex between Nb474 mutant R53A,D125A and Trypanosoma congolense fructose-1,6-bisphosphate aldolase

Components

Fructose-bisphosphate aldolase
Nb474 mutant R53A,D125A

Keywords

LYASE / COMPLEX / NANOBODY / ALDOLASE

Function / homology

Function and homology information

fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / cytoplasm
Similarity search - Function

Biological species

Trypanosoma congolense IL3000 (eukaryote)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.751 Å

Authors

McNae, I.W. / Dornan, J. / Walkinshaw, M.D.

Funding support

United Kingdom, 2items

Citation

Journal: To Be Published
Title: The role of water in tuning nanobody-antigen recognition
Authors: Hacisuleyman, A. / Dorna, J. / McNae, I. / Wear, M. / Bilal, T. / Yuan, M. / Michels, P.A.M. / Pinto Torres, J.E. / Magez, S. / Sterckx, Y.G.J. / Erman, E. / Walkinshaw, M.D.

History

Deposition	Sep 21, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 1, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gv3.cif.gz	944.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9gv3.ent.gz	647.4 KB	Display	PDB format
PDBx/mmJSON format	9gv3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gv3_validation.pdf.gz	513.5 KB	Display	wwPDB validaton report
Full document	9gv3_full_validation.pdf.gz	538.4 KB	Display
Data in XML	9gv3_validation.xml.gz	97.7 KB	Display
Data in CIF	9gv3_validation.cif.gz	131.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gv/9gv3 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/9gv3	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (5)

Deposited unit

A: Fructose-bisphosphate aldolase

B: Fructose-bisphosphate aldolase

C: Fructose-bisphosphate aldolase

D: Fructose-bisphosphate aldolase

E: Nb474 mutant R53A,D125A

F: Nb474 mutant R53A,D125A

G: Nb474 mutant R53A,D125A

H: Nb474 mutant R53A,D125A

hetero molecules

234 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	203.495, 111.166, 123.244
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

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

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	ASP	ASP	2 - 358	2 - 358
2	1	1	ASP	ASP	2 - 358	2 - 358
3	2	2	LYS	LYS	2 - 360	2 - 360
4	2	2	LYS	LYS	2 - 360	2 - 360
5	3	3	ASP	ASP	2 - 358	2 - 358
6	3	3	ASP	ASP	2 - 358	2 - 358
7	4	4	ASP	ASP	2 - 358	2 - 358
8	4	4	ASP	ASP	2 - 358	2 - 358
9	5	5	ASP	ASP	2 - 359	2 - 359
10	5	5	ASP	ASP	2 - 359	2 - 359
11	6	6	ASP	ASP	2 - 358	2 - 358
12	6	6	ASP	ASP	2 - 358	2 - 358
13	7	7	LEU	LEU	2 - 138	2 - 138
14	7	7	LEU	LEU	2 - 138	2 - 138
15	8	8	LEU	LEU	2 - 138	2 - 138
16	8	8	LEU	LEU	2 - 138	2 - 138
17	9	9	LEU	LEU	2 - 138	2 - 138
18	9	9	LEU	LEU	2 - 138	2 - 138
19	10	10	LEU	LEU	2 - 138	2 - 138
20	10	10	LEU	LEU	2 - 138	2 - 138
21	11	11	LEU	LEU	2 - 138	2 - 138
22	11	11	LEU	LEU	2 - 138	2 - 138
23	12	12	LEU	LEU	2 - 138	2 - 138
24	12	12	LEU	LEU	2 - 138	2 - 138

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
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24

#1: Protein	Fructose-bisphosphate aldolase Mass: 42708.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma congolense IL3000 (eukaryote) Gene: TCIL3000_10_4760 / Production host: Escherichia coli (E. coli) / References: UniProt: G0UWE7, fructose-bisphosphate aldolase
#2: Protein	Nb474 mutant R53A,D125A Mass: 15670.010 Da / Num. of mol.: 4 / Mutation: R53A,D125A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₂H₃O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1343 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium cacodylate pH 6.5, 100mM, PEG 8K 10-15%, 200mM magnesium acetate.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6702 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.6702 Å / Relative weight: 1
Reflection	Resolution: 1.75→97.558 Å / Num. obs: 999301 / % possible obs: 87.6 % / Redundancy: 5.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.117 / R_pim(I) all: 0.055 / R_rim(I) all: 0.135 / Net I/σ(I): 9.2
Reflection shell	Resolution: 1.751→1.915 Å / Redundancy: 4.4 % / R_merge(I) obs: 1.058 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 43767 / CC_1/2: 0.533 / R_pim(I) all: 0.525 / % possible all: 64.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
xia2		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.751→97.558 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.959 / SU B: 5.239 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.112
Details: Hydrogens have been used if present in the input file

	R_factor	Num. reflection	% reflection
R_free	0.1882	9820	4.979 %
R_work	0.1598	187393	-
all	0.161	-	-
obs	-	197213	70.488 %

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: 32.24 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.241 Å²	-0 Å²	0 Å²
2-	-	0.166 Å²	0 Å²
3-	-	-	0.075 Å²

Refinement step

Cycle: LAST / Resolution: 1.751→97.558 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15243	0	22	1343	16608

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	15639
X-RAY DIFFRACTION	r_angle_refined_deg	2.224	1.83	21204
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.575	5	2011
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.76	5	140
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.299	10	2586
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.33	10	688
X-RAY DIFFRACTION	r_chiral_restr	0.142	0.2	2335
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	11980
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	7466
X-RAY DIFFRACTION	r_nbtor_refined	0.311	0.2	10981
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	1399
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.191	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.236	0.2	30
X-RAY DIFFRACTION	r_mcbond_it	2.635	2.024	7994
X-RAY DIFFRACTION	r_mcangle_it	3.672	3.608	9987
X-RAY DIFFRACTION	r_scbond_it	4.874	2.364	7645
X-RAY DIFFRACTION	r_scangle_it	6.628	4.117	11207
X-RAY DIFFRACTION	r_lrange_it	7.91	23.353	24812
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.055	0.05	12059
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.057	0.05	12094
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.059	0.05	12002
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.054	0.05	12061
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.049	0.05	12153
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.057	0.05	12051
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.076	0.05	4269
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.066	0.05	4258
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.095	0.05	4118
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.076	0.05	4223
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.094	0.05	4138
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.11	0.05	4051

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	0.0547	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0547	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05725	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.05725	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05945	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05945	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.05395	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.05395	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.04933	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.04933	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.05656	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.05656	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.07573	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.07573	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.0656	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.0656	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.09452	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.09452	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.07636	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.07636	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.09443	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.09443	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.1098	0.05009
12	24	A	X-RAY DIFFRACTION	Local ncs	0.1098	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
1.751-1.796	0.324	57	0.276	965	0.278	20514	0.924	0.947	4.982	0.274
1.796-1.846	0.292	131	0.275	2412	0.276	20012	0.946	0.948	12.7074	0.272
1.846-1.899	0.272	241	0.266	4156	0.266	19436	0.947	0.951	22.623	0.26
1.899-1.958	0.27	458	0.252	8517	0.253	18962	0.945	0.956	47.3315	0.245
1.958-2.022	0.264	691	0.244	14307	0.245	18358	0.95	0.958	81.6973	0.235
2.022-2.093	0.26	841	0.227	15545	0.229	17718	0.954	0.964	92.4822	0.215
2.093-2.172	0.232	796	0.206	15182	0.207	17143	0.964	0.972	93.2042	0.19
2.172-2.26	0.208	781	0.185	14532	0.186	16492	0.972	0.978	92.8511	0.165
2.26-2.361	0.214	687	0.174	13962	0.176	15862	0.972	0.981	92.3528	0.152
2.361-2.476	0.198	693	0.162	13283	0.164	15179	0.976	0.983	92.0746	0.14
2.476-2.61	0.2	674	0.156	12526	0.158	14433	0.975	0.985	91.4571	0.135
2.61-2.768	0.193	628	0.15	11834	0.152	13693	0.978	0.987	91.01	0.131
2.768-2.959	0.181	631	0.154	10984	0.155	12873	0.98	0.986	90.2276	0.137
2.959-3.196	0.192	512	0.153	10228	0.155	12030	0.977	0.986	89.2768	0.139
3.196-3.5	0.171	470	0.145	9248	0.146	11077	0.982	0.988	87.7313	0.139
3.5-3.913	0.162	428	0.133	8470	0.134	10064	0.985	0.99	88.4142	0.133
3.913-4.517	0.13	380	0.12	7411	0.121	8923	0.99	0.992	87.3137	0.126
4.517-5.529	0.153	306	0.119	6315	0.121	7605	0.987	0.992	87.0611	0.129
5.529-7.807	0.184	259	0.163	4845	0.164	5953	0.983	0.987	85.7383	0.172
7.807-97.558	0.159	156	0.161	2672	0.161	3456	0.985	0.981	81.8287	0.215

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	0.676	0.0828	-0.3204	0.733	0.1594	0.6911	-0.0714	0.0186	-0.0438	-0.0058	0.0291	-0.1041	0.0687	0.0801	0.0423	0.042	-0.0091	0.0102	0.0205	0.0023	0.0213	-16.2592	40.1585	-37.1531
2	0.6907	0.2697	0.0727	0.5689	0.1126	0.8883	-0.0675	0.1217	0.0634	-0.096	0.0421	0.142	-0.0289	-0.1209	0.0254	0.0506	-0.023	-0.0145	0.0613	0.0085	0.0384	-53.3731	49.3546	-42.8198
3	0.7008	-0.169	0.0733	0.7661	0.3002	0.8984	-0.0602	-0.0604	0.1424	0.0486	0.0969	-0.1277	-0.0636	0.1728	-0.0367	0.0641	0.0206	-0.0167	0.0545	-0.0255	0.0411	-18.7768	68.2317	-6.0391
4	0.89	-0.0837	-0.3627	0.2689	0.093	0.6854	-0.0525	-0.041	-0.0286	0.0597	0.0401	0.0757	0.0633	-0.0025	0.0124	0.0819	0.0164	0.0149	0.0092	0.012	0.0219	-54.5076	53.7841	-1.562
5	1.5299	-0.3327	-0.5543	2.0919	1.5819	2.9512	0.0531	0.066	0.0176	0.0112	-0.0244	-0.0923	0.1397	-0.018	-0.0287	0.07	0.0273	0.0479	0.0843	0.0458	0.0498	5.1405	28.4616	-68.373
6	1.2289	0.3457	0.2488	1.7283	-0.6576	3.7354	-0.0026	0.1721	-0.1475	-0.2376	0.0141	-0.1932	0.1718	0.1463	-0.0115	0.1047	-0.0324	-0.0119	0.1047	-0.0011	0.1548	-74.3218	35.8108	-74.2965
7	1.4493	-0.1252	0.1609	1.6359	1.4572	2.9684	0.039	0.0937	-0.0325	-0.0368	0.0474	-0.1293	-0.1203	0.2489	-0.0864	0.1286	-0.0084	-0.0551	0.2337	-0.0422	0.0923	0.6254	83.331	25.3131
8	1.3806	-0.0991	-0.5076	1.2987	0.0184	3.2754	0.0322	-0.0482	-0.0102	0.0581	0.0123	0.0265	0.0675	-0.109	-0.0445	0.0627	0.0011	0.0335	0.0079	0.0079	0.0828	-79.913	61.502	29.0965

Refinement TLS group

Selection: ALL

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