PDB-9c9k: Anti-OspA Fab 319-33

ID or keywords:

Entry

Database: PDB / ID: 9c9k

Title

Anti-OspA Fab 319-33

Components

(319-33 monoclonal Fab ...) x 2

Keywords

IMMUNE SYSTEM / human anti-OspA antibody

Function / homology

IMIDAZOLE

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.601 Å

Authors

Rudolph, M.J. / Mantis, N.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Anti-OspA Fab 319-33
Authors: Rudolph, M.J. / Mantis, N.

History

Deposition	Jun 14, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 27, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9c9k.cif.gz	261.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9c9k.ent.gz	212.4 KB	Display	PDB format
PDBx/mmJSON format	9c9k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9c9k_validation.pdf.gz	460.8 KB	Display	wwPDB validaton report
Full document	9c9k_full_validation.pdf.gz	461.5 KB	Display
Data in XML	9c9k_validation.xml.gz	26.9 KB	Display
Data in CIF	9c9k_validation.cif.gz	37.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/9c9k ftp://data.pdbj.org/pub/pdb/validation_reports/c9/9c9k	HTTPS FTP

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Related structure data

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) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

H: 319-33 monoclonal Fab Heavy Chain

L: 319-33 monoclonal Fab Light Chain

hetero molecules

50.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	121.747, 121.747, 67.389
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

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Antibody , 2 types, 2 molecules HL

#1: Antibody	319-33 monoclonal Fab Heavy Chain Mass: 24094.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	319-33 monoclonal Fab Light Chain Mass: 23360.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 5 types, 446 molecules

#3: Chemical	... ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₅N₂
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.63 Å³/Da / Density % sol: 53.25 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 200 mM Zinc Acetate, 100 mM Imidazole pH 8.0, 2.5 M NaCl

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 66957 / % possible obs: 99.8 % / Redundancy: 9.4 % / CC_1/2: 0.85 / Net I/σ(I): 4.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.6-1.63	10.4	1.656	3287	0.557	0.846	0.527	1.739	0.615	99.6
1.63-1.66	10.4	1.429	3298	0.617	0.874	0.455	1.501	0.643	99.7
1.66-1.69	10.1	1.277	3303	0.689	0.903	0.413	1.344	0.657	99.7
1.69-1.72	9.9	1.067	3271	0.731	0.919	0.349	1.124	0.671	100
1.72-1.76	9.6	0.835	3340	0.825	0.951	0.278	0.881	0.718	99.8
1.76-1.8	9.3	0.715	3275	0.846	0.957	0.244	0.757	0.752	99.9
1.8-1.85	8.5	0.581	3297	0.851	0.959	0.208	0.618	0.816	99.5
1.85-1.9	8.8	0.479	3322	0.913	0.977	0.168	0.509	0.844	99.9
1.9-1.95	9.8	0.373	3321	0.965	0.991	0.122	0.393	0.904	100
1.95-2.02	9.8	0.313	3337	0.966	0.991	0.103	0.33	0.989	99.9
2.02-2.09	9.6	0.257	3307	0.977	0.994	0.086	0.271	1.051	100
2.09-2.17	9.5	0.212	3347	0.983	0.996	0.071	0.224	1.112	100
2.17-2.27	9.3	0.188	3336	0.987	0.997	0.063	0.198	1.148	99.9
2.27-2.39	9.1	0.158	3358	0.99	0.997	0.054	0.167	1.208	99.9
2.39-2.54	8.6	0.136	3343	0.99	0.998	0.048	0.144	1.282	99.8
2.54-2.74	8.1	0.111	3349	0.992	0.998	0.04	0.119	1.272	99.3
2.74-3.01	9.7	0.092	3379	0.996	0.999	0.031	0.097	1.353	100
3.01-3.45	9.7	0.072	3408	0.997	0.999	0.024	0.076	1.179	100
3.45-4.34	9.2	0.061	3458	0.997	0.999	0.021	0.065	1.143	99.9
4.34-50	8.4	0.059	3621	0.997	0.999	0.021	0.062	1.036	99.3

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.601→45.172 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1995	3294	4.92 %
R_work	0.1716	-	-
obs	0.173	66895	99.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.601→45.172 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3226	0	95	382	3703

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3407
X-RAY DIFFRACTION	f_angle_d	1.074	4636
X-RAY DIFFRACTION	f_dihedral_angle_d	11.01	2022
X-RAY DIFFRACTION	f_chiral_restr	0.065	510
X-RAY DIFFRACTION	f_plane_restr	0.007	595

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 (%)
1.601-1.6235	0.3031	122	0.2677	2621	X-RAY DIFFRACTION	99
1.6235-1.6477	0.2412	135	0.2569	2589	X-RAY DIFFRACTION	100
1.6477-1.6735	0.2637	144	0.2509	2607	X-RAY DIFFRACTION	100
1.6735-1.7009	0.2741	132	0.2445	2613	X-RAY DIFFRACTION	100
1.7009-1.7302	0.2782	142	0.2203	2621	X-RAY DIFFRACTION	100
1.7302-1.7617	0.2204	138	0.2088	2627	X-RAY DIFFRACTION	100
1.7617-1.7956	0.2653	134	0.2094	2595	X-RAY DIFFRACTION	100
1.7956-1.8322	0.2302	117	0.2081	2654	X-RAY DIFFRACTION	100
1.8322-1.8721	0.2344	129	0.2021	2624	X-RAY DIFFRACTION	99
1.8721-1.9156	0.234	130	0.1889	2628	X-RAY DIFFRACTION	100
1.9156-1.9635	0.231	135	0.1712	2618	X-RAY DIFFRACTION	100
1.9635-2.0166	0.1675	138	0.1672	2646	X-RAY DIFFRACTION	100
2.0166-2.0759	0.1968	125	0.1602	2634	X-RAY DIFFRACTION	100
2.0759-2.1429	0.1868	145	0.1601	2640	X-RAY DIFFRACTION	100
2.1429-2.2195	0.2074	148	0.1611	2613	X-RAY DIFFRACTION	100
2.2195-2.3084	0.1827	141	0.1581	2655	X-RAY DIFFRACTION	100
2.3084-2.4135	0.2013	148	0.1625	2642	X-RAY DIFFRACTION	100
2.4135-2.5407	0.2055	144	0.1658	2647	X-RAY DIFFRACTION	100
2.5407-2.6999	0.2162	129	0.1685	2656	X-RAY DIFFRACTION	99
2.6999-2.9083	0.1959	135	0.1722	2679	X-RAY DIFFRACTION	100
2.9083-3.2009	0.2068	117	0.1706	2719	X-RAY DIFFRACTION	100
3.2009-3.6639	0.1951	147	0.1598	2694	X-RAY DIFFRACTION	100
3.6639-4.6154	0.1545	160	0.1361	2722	X-RAY DIFFRACTION	100
4.6154-45.172	0.197	159	0.1833	2857	X-RAY DIFFRACTION	99

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	4.1962	-1.9531	-2.71	5.8695	5.1285	6.8723	-0.1549	-0.1579	-0.7534	0.18	-0.1617	0.1555	0.2541	-0.2275	0.3057	0.1898	-0.0264	0.0162	0.1681	0.1076	0.3596	-2.2866	16.4522	21.7069
2	5.8384	0.362	0.0908	3.5115	-0.2116	0.9757	0.1119	-0.277	-0.2124	0.425	-0.0094	0.2441	-0.0034	-0.1344	-0.0079	0.1498	-0.012	-0.0092	0.1554	0.0394	0.1499	-7.4627	28.824	23.9347
3	6.1274	0.5044	-1.4115	3.7558	-0.0315	2.3247	0.0959	0.2222	-0.3901	-0.2574	-0.044	0.1509	0.1067	-0.167	-0.0237	0.1578	-0.0014	-0.0398	0.1388	-0.0019	0.1544	-6.353	28.0127	13.5277
4	3.4447	-0.5486	-0.4918	2.7638	0.6298	0.5928	-0.025	-0.0915	-0.4781	0.1181	-0.018	0.2061	0.1079	-0.058	0.0517	0.135	-0.0171	-0.0136	0.1498	0.0481	0.1919	-4.4114	24.2127	20.118
5	4.6527	-0.4961	0.0071	1.103	0.0587	0.4711	-0.0649	-0.1032	-0.2826	0.065	0.0316	0.1749	0.0939	0.0775	0.0118	0.1977	0.0092	0.0077	0.1811	0.0213	0.1819	25.1192	13.438	17.587
6	3.6897	3.9958	2.1027	4.9238	1.2057	3.082	0.3147	-1.16	-0.7559	0.3643	-0.1984	-0.151	0.5375	-0.0937	-0.0735	0.3762	0.0216	0.0156	0.3239	0.1025	0.2679	30.233	7.125	24.0246
7	7.3606	0.2176	4.1485	0.2577	0.6135	3.7823	0.1689	0.4335	-0.1969	-0.0583	0.0688	-0.1091	0.066	0.2531	-0.1984	0.1889	-0.0177	0.0149	0.1644	0.0029	0.1552	13.9022	43.7801	15.6085
8	6.9938	-1.5352	3.575	1.5056	-1.1622	4.0478	-0.0534	-0.0218	0.2737	-0.1659	-0.0245	0.1388	-0.0502	0.0165	0.1052	0.1268	0.0001	-0.01	0.0811	-0.0379	0.1169	3.3158	44.51	16.2643
9	3.007	0.669	0.4141	1.8748	0.7762	1.8552	0.0404	-0.2565	0.0386	0.1553	-0.1277	-0.0213	-0.078	-0.0016	0.0466	0.1606	-0.0018	-0.0111	0.2014	-0.0022	0.1316	6.3181	43.5669	24.6175
10	3.4016	1.3513	1.572	1.5628	0.6513	1.2726	0.089	-0.0386	-0.0398	0.0819	-0.0122	-0.0701	0.0292	0.0183	-0.0907	0.1576	0.0016	-0.0081	0.1485	0.0041	0.1142	7.5344	39.6407	19.6432
11	4.474	-3.9421	-4.6767	3.4727	4.1187	4.8863	-0.0743	-0.4286	0.8484	0.0063	0.3987	-0.4338	-0.1888	0.3142	-0.2441	0.1399	-0.0018	-0.0162	0.1805	-0.0325	0.2476	29.1859	38.1417	17.7688
12	1.4927	-0.8547	-0.6813	5.6406	2.856	3.0924	0.0498	0.0605	0.0113	-0.1055	-0.1465	0.1069	0.0977	-0.0142	0.0862	0.1511	0.0263	-0.0129	0.1985	-0.0118	0.1501	32.1598	19.0749	6.4798
13	1.4633	-1.1562	-1.2374	6.8424	4.1904	3.6796	-0.0615	-0.0549	0.075	-0.1604	0.111	-0.1432	0.0507	0.1803	-0.0547	0.1568	0.0468	-0.0535	0.2252	0.0129	0.124	34.8611	20.8812	6.5495

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 2 through 25 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 26 through 39 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 40 through 68 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 69 through 109 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 110 through 191 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 192 through 216 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 1 through 18 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 19 through 39 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 40 through 76 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 77 through 103 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 104 through 114 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 115 through 164 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 165 through 214 )

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