PDB-9hi4: Structure of FI6-focused design_03 scaffold in complex with FI6-Fab

ID or keywords:

Entry

Database: PDB / ID: 9hi4

Title

Structure of FI6-focused design_03 scaffold in complex with FI6-Fab

Components

(FI6-focused design_03) x 2
FI6 Fab Heavy chain
FI6 Fab Light chain

Keywords

BIOSYNTHETIC PROTEIN / scaffold / influenza

Function / homology

ACETATE ION

Function and homology information

Biological species

Homo sapiens (human)

Bacteroides uniformis ATCC 8492 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Cramer, J.T. / Krey, T.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structure of FI6-focused design_03 scaffold in complex with FI6-Fab
Authors: Cramer, J.T. / Krey, T.

History

Deposition	Nov 24, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hi4.cif.gz	675.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9hi4.ent.gz	457.3 KB	Display	PDB format
PDBx/mmJSON format	9hi4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hi4_validation.pdf.gz	469.5 KB	Display	wwPDB validaton report
Full document	9hi4_full_validation.pdf.gz	471.8 KB	Display
Data in XML	9hi4_validation.xml.gz	70.8 KB	Display
Data in CIF	9hi4_validation.cif.gz	98.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hi/9hi4 ftp://data.pdbj.org/pub/pdb/validation_reports/hi/9hi4	HTTPS FTP

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Related structure data

Related structure data	3ztjS 4iyjS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: FI6 Fab Heavy chain

B: FI6 Fab Light chain

C: FI6-focused design_03

D: FI6-focused design_03

K: FI6 Fab Heavy chain

L: FI6 Fab Light chain

hetero molecules

149 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: FI6 Fab Heavy chain

B: FI6 Fab Light chain

D: FI6-focused design_03

hetero molecules

defined by author
Evidence: gel filtration
74.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: FI6-focused design_03

K: FI6 Fab Heavy chain

L: FI6 Fab Light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.230, 78.140, 118.720
Angle α, β, γ (deg.)	90.000, 100.600, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 2 types, 2 molecules CD

#3: Protein	FI6-focused design_03 Mass: 25012.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis ATCC 8492 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Protein	FI6-focused design_03 Mass: 24932.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis ATCC 8492 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria)

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Antibody , 2 types, 4 molecules AKBL

#1: Antibody	FI6 Fab Heavy chain Mass: 25368.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody	FI6 Fab Light chain Mass: 24177.760 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)

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Non-polymers , 3 types, 1388 molecules

#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₂H₃O₂
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1385 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.79 Å³/Da / Density % sol: 55.92 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 13% (w/V) PEG 8000, 20% (V/V) Glycerol, 80 mM Sodium cacodylate pH 6.5, 160 mM Calcium acetate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 2 / Wavelength: 0.980107 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 20, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.980107 Å / Relative weight: 1

Reflection

Resolution: 1.7→44.84 Å / Num. obs: 180116 / % possible obs: 99.9 % / Redundancy: 6.945 % / B_iso Wilson estimate: 35.294 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.073 / R_rim(I) all: 0.079 / Χ²: 0.872 / Net I/σ(I): 13.79

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.74	7.094	1.747	1.08	13285	0.585	1.885	99.9
1.74-1.79	7.064	1.303	1.5	12937	0.683	1.406	100
1.79-1.84	6.98	0.993	1.99	12581	0.806	1.073	100
1.84-1.9	6.856	0.723	2.71	12236	0.89	0.782	100
1.9-1.96	6.482	0.509	3.68	11840	0.926	0.553	100
1.96-2.03	7.087	0.397	5	11499	0.964	0.428	99.9
2.03-2.11	7.102	0.298	6.57	11037	0.978	0.322	100
2.11-2.19	6.997	0.227	8.4	10626	0.985	0.245	100
2.19-2.29	6.567	0.183	9.62	10258	0.988	0.199	99.9
2.29-2.4	7.131	0.149	12.08	9770	0.992	0.161	99.9
2.4-2.53	7.28	0.121	14.89	9300	0.995	0.13	100
2.53-2.69	7.203	0.097	18	8824	0.996	0.104	99.9
2.69-2.87	7.113	0.077	22.15	8256	0.997	0.083	99.9
2.87-3.1	6.917	0.059	27.46	7713	0.998	0.064	100
3.1-3.4	6.34	0.046	32.5	7150	0.998	0.05	99.9
3.4-3.8	7.031	0.039	40.03	6414	0.999	0.042	99.8
3.8-4.39	6.866	0.035	43.62	5701	0.999	0.038	99.9
4.39-5.38	6.542	0.033	44.37	4826	0.999	0.036	99.8
5.38-7.6	7.257	0.034	44.76	3769	0.999	0.037	99.8
7.6-44.84	6.531	0.027	47.64	2094	0.999	0.03	98.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.96 Å	46.75 Å
Translation	2.96 Å	46.75 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER	2.8.2	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ZTJ, 4iyj

3ztj

4iyj

Resolution: 2→44.84 Å / SU ML: 0.1741 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.4803
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.196	5541	5 %	RANDOM
R_work	0.1698	105276	-	-
obs	0.1711	110817	99.87 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 30.72 Å²

Refinement step

Cycle: LAST / Resolution: 2→44.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10000	0	6	1385	11391

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	10358
X-RAY DIFFRACTION	f_angle_d	0.6336	14133
X-RAY DIFFRACTION	f_chiral_restr	0.0464	1587
X-RAY DIFFRACTION	f_plane_restr	0.0047	1833
X-RAY DIFFRACTION	f_dihedral_angle_d	5.7708	1452

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 (%)
2-2.02	0.2304	182	0.1945	3460	X-RAY DIFFRACTION	99.86
2.02-2.05	0.2355	183	0.1929	3503	X-RAY DIFFRACTION	99.81
2.05-2.07	0.2362	185	0.1972	3500	X-RAY DIFFRACTION	99.92
2.07-2.1	0.2271	181	0.1883	3450	X-RAY DIFFRACTION	99.89
2.1-2.13	0.231	186	0.1911	3524	X-RAY DIFFRACTION	99.92
2.13-2.15	0.2395	185	0.1875	3513	X-RAY DIFFRACTION	99.92
2.15-2.19	0.2084	184	0.1861	3488	X-RAY DIFFRACTION	99.84
2.19-2.22	0.2363	182	0.1884	3458	X-RAY DIFFRACTION	99.97
2.22-2.25	0.2267	184	0.1911	3487	X-RAY DIFFRACTION	99.97
2.25-2.29	0.2467	185	0.1917	3523	X-RAY DIFFRACTION	99.87
2.29-2.33	0.2367	183	0.1868	3479	X-RAY DIFFRACTION	99.92
2.33-2.37	0.2256	186	0.1907	3537	X-RAY DIFFRACTION	99.87
2.37-2.42	0.2429	181	0.1864	3459	X-RAY DIFFRACTION	99.89
2.42-2.47	0.2639	183	0.1855	3487	X-RAY DIFFRACTION	99.92
2.47-2.52	0.2206	186	0.1841	3535	X-RAY DIFFRACTION	99.92
2.52-2.58	0.231	185	0.1807	3498	X-RAY DIFFRACTION	99.97
2.58-2.64	0.2257	183	0.1832	3490	X-RAY DIFFRACTION	100
2.64-2.71	0.2441	185	0.1886	3513	X-RAY DIFFRACTION	99.95
2.71-2.79	0.2266	186	0.1911	3538	X-RAY DIFFRACTION	99.97
2.79-2.88	0.2394	184	0.1958	3484	X-RAY DIFFRACTION	99.95
2.88-2.99	0.2385	183	0.1867	3476	X-RAY DIFFRACTION	99.92
2.99-3.11	0.1788	185	0.1747	3528	X-RAY DIFFRACTION	99.92
3.11-3.25	0.2334	187	0.1721	3546	X-RAY DIFFRACTION	99.92
3.25-3.42	0.1928	184	0.1705	3498	X-RAY DIFFRACTION	99.92
3.42-3.63	0.1627	186	0.1611	3531	X-RAY DIFFRACTION	99.89
3.63-3.91	0.1923	185	0.1477	3519	X-RAY DIFFRACTION	99.92
3.91-4.31	0.1304	187	0.1394	3550	X-RAY DIFFRACTION	99.84
4.31-4.93	0.127	186	0.1307	3528	X-RAY DIFFRACTION	99.76
4.93-6.21	0.1718	187	0.1563	3556	X-RAY DIFFRACTION	99.97
6.21-44.84	0.1806	192	0.1723	3618	X-RAY DIFFRACTION	98.91

Refinement TLS params.

Method: refined / Origin x: 0.676047375859 Å / Origin y: 39.1694493569 Å / Origin z: 15.6400315897 Å

	11	12	13	21	22	23	31	32	33
T	0.252758123995 Å²	0.0134158774891 Å²	-0.0114116615433 Å²	-	0.19149046772 Å²	0.00815646935343 Å²	-	-	0.252860393665 Å²
L	0.382184281967 °²	0.0074412735644 °²	-0.534831040791 °²	-	-0.00829743300996 °²	0.00785067737672 °²	-	-	0.809391767394 °²
S	0.0175736573839 Å °	-0.0432121867044 Å °	0.00257128675376 Å °	-0.00185453188764 Å °	-0.0116456346175 Å °	0.00303603703636 Å °	-0.0280010302293 Å °	0.0571963083475 Å °	-0.00372639393164 Å °

Refinement TLS group

Selection details: all

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Protein , 2 types, 2 molecules CD

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Non-polymers , 3 types, 1388 molecules

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Non-polymers , 3 types, 1388 molecules

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