PDB-9hi6: Structure of scaffold FI6-focused design_04 in complex with FI6-Fab

ID or keywords:

Entry

Database: PDB / ID: 9hi6

Title

Structure of scaffold FI6-focused design_04 in complex with FI6-Fab

Components

FI6 Fab Heavy Chain
FI6-Fab Light Chain
FI6-focused design_04

Keywords

BIOSYNTHETIC PROTEIN / scaffold / influenza

Function / homology

CITRIC ACID / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Homo sapiens (human)

Bacteroides uniformis ATCC 8492 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.5 Å

Authors

Cramer, J.T. / Krey, T.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structure of scaffold FI6-focused design_04 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	9hi6.cif.gz	337.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9hi6.ent.gz	224.5 KB	Display	PDB format
PDBx/mmJSON format	9hi6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hi/9hi6 ftp://data.pdbj.org/pub/pdb/validation_reports/hi/9hi6	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

H: FI6 Fab Heavy Chain

L: FI6-Fab Light Chain

A: FI6-focused design_04

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	71.213, 47.869, 107.093
Angle α, β, γ (deg.)	90.000, 106.130, 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 , 1 types, 1 molecules A

#3: Protein	FI6-focused design_04 Mass: 24599.826 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, 2 molecules HL

#1: Antibody	FI6 Fab Heavy Chain Mass: 25425.523 Da / Num. of mol.: 1 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: 23976.578 Da / Num. of mol.: 1 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, 747 molecules

#4: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₆H₈O₇
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.37 Å³/Da / Density % sol: 48.09 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 20%(w/V) PEG3350, 200mM (NH4)2Hcitrate pH 5.0

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 1 / Wavelength: 1.03674 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020

Radiation

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

Radiation wavelength

Wavelength: 1.03674 Å / Relative weight: 1

Reflection

Resolution: 1.5→43.4 Å / Num. obs: 110619 / % possible obs: 99.5 % / Redundancy: 6.863 % / B_iso Wilson estimate: 26.738 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.095 / R_rim(I) all: 0.103 / Χ²: 0.877 / Net I/σ(I): 11.53

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
1.5-1.54	6.826	1.193	1.43	7999	0.597	1.291	97.8
1.54-1.58	7.027	0.995	1.79	7906	0.726	1.074	99.3
1.58-1.63	6.977	0.82	2.28	7672	0.78	0.886	99.3
1.63-1.68	6.914	0.681	2.76	7460	0.856	0.736	99.3
1.68-1.73	6.71	0.56	3.46	7268	0.884	0.607	99.4
1.73-1.79	6.611	0.437	4.49	7021	0.938	0.475	99.6
1.79-1.86	6.67	0.355	5.78	6823	0.959	0.385	99.8
1.86-1.94	7.063	0.287	7.62	6526	0.974	0.31	99.8
1.94-2.02	7.111	0.226	10	6311	0.984	0.244	99.9
2.02-2.12	7.033	0.183	12.29	5995	0.989	0.197	99.9
2.12-2.24	6.913	0.151	14.44	5757	0.991	0.163	99.9
2.24-2.37	6.641	0.126	15.92	5443	0.992	0.136	99.9
2.37-2.54	6.674	0.109	17.93	5112	0.995	0.119	99.9
2.54-2.74	6.725	0.091	20.44	4746	0.995	0.099	99.7
2.74-3	7.222	0.073	25.09	4415	0.997	0.079	99.9
3-3.36	7.115	0.059	29.25	3965	0.998	0.064	99.9
3.36-3.88	6.885	0.05	32.76	3525	0.998	0.054	99.8
3.88-4.75	6.43	0.046	33.66	3014	0.998	0.05	99.8
4.75-6.71	6.685	0.045	34.14	2335	0.998	0.049	99.8
6.71-43.4	6.626	0.043	35.69	1326	0.998	0.047	99

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	1.5 Å	43.4 Å
Translation	1.5 Å	43.4 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	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ztj, 4iyj

3ztj

4iyj

Resolution: 1.5→43.4 Å / SU ML: 0.1791 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2037	5523	5 %
R_work	0.1775	104944	-
obs	0.1788	110467	99.46 %

Solvent computation

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

Displacement parameters

B_iso mean: 29.97 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→43.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4947	0	40	743	5730

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0083	5141
X-RAY DIFFRACTION	f_angle_d	0.9615	7015
X-RAY DIFFRACTION	f_chiral_restr	0.0644	785
X-RAY DIFFRACTION	f_plane_restr	0.0082	910
X-RAY DIFFRACTION	f_dihedral_angle_d	10.2051	728

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 (%)
1.5-1.52	0.32	177	0.2801	3361	X-RAY DIFFRACTION	96.51
1.52-1.54	0.2569	180	0.2565	3426	X-RAY DIFFRACTION	98.55
1.54-1.56	0.2489	183	0.2521	3453	X-RAY DIFFRACTION	98.16
1.56-1.57	0.2596	180	0.2414	3433	X-RAY DIFFRACTION	99.34
1.57-1.6	0.288	182	0.236	3463	X-RAY DIFFRACTION	98.06
1.6-1.62	0.2585	183	0.2264	3484	X-RAY DIFFRACTION	99.81
1.62-1.64	0.2926	181	0.2718	3434	X-RAY DIFFRACTION	99.26
1.64-1.66	0.3419	182	0.278	3476	X-RAY DIFFRACTION	98.81
1.66-1.69	0.3081	184	0.2486	3490	X-RAY DIFFRACTION	99.76
1.69-1.72	0.2703	182	0.2324	3455	X-RAY DIFFRACTION	98.86
1.72-1.75	0.2347	185	0.2089	3516	X-RAY DIFFRACTION	99.84
1.75-1.78	0.2214	183	0.1924	3497	X-RAY DIFFRACTION	99.22
1.78-1.81	0.2078	182	0.1849	3447	X-RAY DIFFRACTION	99.86
1.81-1.85	0.2238	183	0.1814	3487	X-RAY DIFFRACTION	99.51
1.85-1.89	0.1987	186	0.1818	3518	X-RAY DIFFRACTION	99.89
1.89-1.94	0.2072	182	0.1816	3457	X-RAY DIFFRACTION	99.7
1.94-1.98	0.2192	187	0.1888	3550	X-RAY DIFFRACTION	99.92
1.98-2.04	0.2301	183	0.1937	3470	X-RAY DIFFRACTION	99.81
2.04-2.1	0.2021	185	0.1796	3537	X-RAY DIFFRACTION	99.95
2.1-2.17	0.2238	185	0.1695	3508	X-RAY DIFFRACTION	99.95
2.17-2.24	0.1967	184	0.1688	3503	X-RAY DIFFRACTION	99.95
2.24-2.33	0.225	184	0.1692	3503	X-RAY DIFFRACTION	100
2.33-2.44	0.194	187	0.1766	3544	X-RAY DIFFRACTION	99.92
2.44-2.57	0.2209	184	0.1742	3496	X-RAY DIFFRACTION	99.76
2.57-2.73	0.2037	186	0.1803	3526	X-RAY DIFFRACTION	99.87
2.73-2.94	0.1907	186	0.173	3545	X-RAY DIFFRACTION	99.95
2.94-3.23	0.1901	187	0.1786	3552	X-RAY DIFFRACTION	99.92
3.23-3.7	0.1933	188	0.1587	3567	X-RAY DIFFRACTION	99.97
3.7-4.66	0.1622	188	0.1385	3569	X-RAY DIFFRACTION	99.89
4.66-43.4	0.1694	194	0.1621	3677	X-RAY DIFFRACTION	99.67

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	5.05650413753	2.19815358803	-3.8567422101	3.1826272384	-1.78674295905	7.51753833313	0.113374672558	-0.378356638002	0.176992769872	0.152786281821	-0.0136402462038	-0.168017305639	-0.224856423422	0.607732936746	-0.154661035554	0.115754303313	0.0198023786146	-0.0256358301593	0.0994291080182	-0.0302665418252	0.130780244056	-6.34005265893	11.6442646904	-31.272196665
2	0.836582510933	-0.0165459070666	-0.0957039590286	0.642520863438	0.685083477749	2.18074190691	-0.0375265497159	0.00291305268845	0.0456459797594	-0.0302309633674	0.056498975044	0.00541350133653	-0.0079961039749	0.149419291678	-0.014739353612	0.117259499401	0.0138423249484	-0.00380510071142	0.108071763777	0.00109778638735	0.133122987114	-7.78143982335	7.30839458061	-44.5557750225
3	1.79721140933	0.437735722308	1.92197374291	0.657231099723	0.41538544331	2.17272587229	-0.0521546018396	-0.557851285648	0.473360238854	0.19033241642	0.250286607133	-0.161762177287	0.0375646479462	0.0185630396142	-0.0594913329488	0.200601036672	0.0985523818368	-0.0315533430148	0.27468685521	-0.108933969573	0.189445506513	-3.71382834334	7.78468445282	-22.7991795539
4	3.94086351349	-1.95494854614	-0.584751851343	5.04308950524	0.801398865295	3.65183323631	-0.395511513973	-1.28508302025	0.421176058672	0.291670218754	0.300733446616	-0.193243485672	-0.135741634668	-0.172467187303	0.0955283266796	0.180150431186	0.0760421620265	-0.0177991557902	0.429474783769	-0.107909133308	0.22612222437	12.8126909592	-0.0721111351174	-9.19731167685
5	8.18657839796	0.628631624188	2.13125592952	2.40754857663	-0.0843170530038	2.02057729842	-0.239827182064	-0.444281595818	0.304604873603	-0.0340292525518	0.0693107107096	-0.189974875622	-0.224091201786	0.137172941903	0.149866354024	0.17888063197	0.0502270820942	-0.00510153332848	0.257419755412	-0.0461550486481	0.126987203841	13.6321080843	1.85738905302	-15.7344636805
6	4.28657728283	-3.00891791512	3.72521907495	2.3838677686	-2.8325054522	3.9324444647	-0.407588942609	-1.16309724415	0.662296144774	0.2078602521	0.0571819775929	0.411009244328	-0.543510416422	-0.279300969496	0.262553537952	0.30350931368	0.0750837578349	-0.118946674042	0.394875182574	-0.203552485521	0.548789164901	12.5465843541	9.21388594025	-11.2970565727
7	4.50390895426	-1.3333269765	-0.00138030773517	1.97482454351	0.0766145568291	1.23958108776	-0.0412318162211	-0.177493143018	-0.157489785094	0.16930822608	0.189643621223	-0.202265908336	0.271427085358	0.554439726903	-0.129106708923	0.201791464324	0.126020569714	-0.0238893550157	0.407935076312	-0.0696921834089	0.228399137308	9.05088508123	-6.97798496648	-47.7442872524
8	7.74430170887	-3.26027308782	7.96170401977	0.996771231852	-3.57698612817	7.33833244364	0.132076589279	0.270955607026	-0.296220280379	0.0158629231017	-0.0251475977137	0.0775404542374	0.118963769673	0.366858582018	-0.111207173826	0.21079812881	0.0814872622565	-0.0262427709169	0.242670305142	-0.0451562875027	0.188502051903	7.76934343623	-10.0710540569	-39.280849523
9	4.47587314714	-0.825569957955	-1.35916795146	2.44865254652	1.41341307808	4.1431268608	-0.115994492218	-0.516979137815	-0.373772278203	0.368151923705	-0.179431832316	0.331288239125	0.496448054879	-0.708822303927	0.227507297168	0.232830327217	-0.0429999326563	0.0849502425762	0.47136862296	0.0449434833141	0.233693527171	11.3513267046	-12.5323433	-11.0088412462
10	3.51808866195	-0.887921854587	-1.15589556882	2.55422455753	0.663257860621	3.93562512577	-0.0817350854588	0.605429983298	-0.116709352622	-0.533694734132	0.048545431242	0.152824967728	0.0446036656874	-0.115090131064	0.0442232282826	0.263608740793	-0.0664223204238	-0.0396867852928	0.216451701759	-0.0272549350612	0.139355225305	-18.8164668574	7.94726361885	-89.0745496409
11	1.79603953406	-1.06389707301	0.263030917897	4.2980783608	-1.13561315375	3.21593762675	-0.099810709066	0.197091095364	-0.230346476146	-0.345426360443	-0.0120569137457	-0.0676341090263	0.479028844995	0.016004893972	0.103678101118	0.202399748322	-0.0373001540416	0.034764999906	0.147073492841	-0.0471111867198	0.161003062429	-9.2289812859	2.84160064657	-83.2654757748
12	6.50616922982	0.335897087	0.107864321869	5.02460931496	-6.60196818989	8.79564730406	-0.0336899165986	0.143694379532	-0.0546291583572	0.0396918818334	-0.202705606822	-0.175696977701	-0.000936336018906	0.447979389982	0.229952424233	0.156337047839	-0.0193239766234	0.0225757990461	0.176844933241	-0.0252211166436	0.124703407393	-2.28339858842	7.41092595501	-77.8786592848
13	1.27439588513	0.167511176559	0.137268845558	1.51579186357	-0.646983463699	1.37744130686	0.0296006226568	-0.0180999311761	0.0607896906219	-0.00187225852535	0.0126365443189	0.144843225263	-0.0340219469969	0.0372049013392	-0.0481072510125	0.124463482558	-0.00680871364019	0.00908901789484	0.0973735751977	-0.020861359232	0.120041329456	-16.7592414429	7.24715868147	-70.1768626841

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	CHAIN 'H' AND (RESID 2 THROUGH 17 )	H	A	2 - 17	2 - 17
2	2	CHAIN 'H' AND (RESID 18 THROUGH 119 )	H	A	18 - 119	18 - 119
3	3	CHAIN 'H' AND (RESID 120 THROUGH 135 )	H	A	120 - 135	120 - 135
4	4	CHAIN 'H' AND (RESID 136 THROUGH 161 )	H	A	136 - 161	136 - 155
5	5	CHAIN 'H' AND (RESID 162 THROUGH 209 )	H	A	162 - 209	156 - 203
6	6	CHAIN 'H' AND (RESID 210 THROUGH 230 )	H	A	210 - 230	204 - 224
7	7	CHAIN 'L' AND (RESID 1 THROUGH 94 )	L	C	1 - 94	1 - 91
8	8	CHAIN 'L' AND (RESID 95 THROUGH 116 )	L	C	95 - 116	92 - 113
9	9	CHAIN 'L' AND (RESID 117 THROUGH 215 )	L	C	117 - 215	114 - 212
10	10	CHAIN 'A' AND (RESID 7 THROUGH 60 )	A	E	7 - 60	2 - 55
11	11	CHAIN 'A' AND (RESID 61 THROUGH 102 )	A	E	61 - 102	56 - 97
12	12	CHAIN 'A' AND (RESID 103 THROUGH 119 )	A	E	103 - 119	98 - 114
13	13	CHAIN 'A' AND (RESID 120 THROUGH 220 )	A	E	120 - 220	115 - 215

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Protein , 1 types, 1 molecules A

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Antibody , 2 types, 2 molecules HL

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Non-polymers , 3 types, 747 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Movie

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Structure viewers

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Viewer log

-
This page

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This web site

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Open data

-
Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 1 molecules A

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Antibody , 2 types, 2 molecules HL

-
Non-polymers , 3 types, 747 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

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Yorodumi