PDB-4x0k: Engineered Fab fragment specific for EYMPME (EE) peptide

ID or keywords:

Entry

Database: PDB / ID: 4x0k

Title

Engineered Fab fragment specific for EYMPME (EE) peptide

Components

Fab fragment heavy chain
Fab fragment light chain

Keywords

IMMUNE SYSTEM / antibody fragment / crystallization chaperone / Fab fragment

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Johnson, J.L. / Lieberman, R.L.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization.
Authors: Johnson, J.L. / Entzminger, K.C. / Hyun, J. / Kalyoncu, S. / Heaner, D.P. / Morales, I.A. / Sheppard, A. / Gumbart, J.C. / Maynard, J.A. / Lieberman, R.L.

History

Deposition	Nov 21, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 22, 2015	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Source and taxonomy Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4x0k.cif.gz	372.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4x0k.ent.gz	304.1 KB	Display	PDB format
PDBx/mmJSON format	4x0k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4x0k_validation.pdf.gz	445.4 KB	Display	wwPDB validaton report
Full document	4x0k_full_validation.pdf.gz	449.7 KB	Display
Data in XML	4x0k_validation.xml.gz	37.9 KB	Display
Data in CIF	4x0k_validation.cif.gz	55.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x0/4x0k ftp://data.pdbj.org/pub/pdb/validation_reports/x0/4x0k	HTTPS FTP

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Related structure data

Related structure data	3sobS S: Starting model for refinement
Similar structure data	1tjg-d 2hfg-d 5u3l-1 6blh-d 3ghe-d 4yaq-1 6vi2-2 1n64-d 5e08-d 5wna-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Fab fragment heavy chain

L: Fab fragment light chain

A: Fab fragment heavy chain

B: Fab fragment light chain

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

1

H: Fab fragment heavy chain

L: Fab fragment light chain

defined by author&software
51.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Fab fragment heavy chain

B: Fab fragment light chain

defined by author&software
51.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.559, 67.131, 71.877
Angle α, β, γ (deg.)	71.30, 78.10, 85.31
Int Tables number	1
Space group name H-M	P1

#1: Antibody	Fab fragment heavy chain Mass: 25854.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	Fab fragment light chain Mass: 25591.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H₂O
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: 2.33 Å³/Da / Density % sol: 47.16 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M HEPES (pH 7.5), 100 mM calcium acetate, 20-26% (w/v) PEG 8000, and 3% 1-propanol

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 11, 2012 / Details: MAR CCD 300

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.04→50 Å / Num. obs: 57696 / % possible obs: 98 % / Redundancy: 3.9 % / R_merge(I) obs: 0.084 / Χ²: 1.634 / Net I/av σ(I): 22.225 / Net I/σ(I): 8.9 / Num. measured all: 226592

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.05-2.09	3.9	0.58	2829	0.886	96.8
2.09-2.12	3.9	0.501	2854	0.86	96.7
2.12-2.16	4	0.432	2838	0.891	97.3
2.16-2.21	4	0.378	2849	0.915	97.3
2.21-2.26	3.9	0.342	2893	0.988	97.3
2.26-2.31	3.9	0.313	2868	1.031	97.4
2.31-2.37	4	0.268	2857	0.998	97.6
2.37-2.43	4	0.244	2922	1.057	97.7
2.43-2.5	4	0.206	2862	1.056	97.8
2.5-2.58	4	0.179	2885	1.147	97.9
2.58-2.68	4	0.156	2872	1.294	98.1
2.68-2.78	4	0.132	2888	1.494	98.3
2.78-2.91	3.9	0.112	2905	1.644	98.4
2.91-3.06	4	0.094	2895	1.937	98.2
3.06-3.25	3.9	0.081	2900	2.239	98.7
3.25-3.51	3.9	0.07	2903	2.6	98.7
3.51-3.86	3.9	0.067	2928	3.071	98.8
3.86-4.42	3.8	0.056	2899	3.224	99
4.42-5.56	3.9	0.047	2923	2.788	99.2
5.56-50	3.9	0.044	2926	2.616	99.5

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-2000		data reduction
PDB_EXTRACT	3.15	data extraction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SOB

3sob

Resolution: 2.04→32.965 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2073	2946	5.11 %	Random selection
R_work	0.1645	-	-	-
obs	0.1667	57673	97.69 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.04→32.965 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6951	0	0	525	7476

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7199
X-RAY DIFFRACTION	f_angle_d	0.88	9768
X-RAY DIFFRACTION	f_dihedral_angle_d	13.065	2590
X-RAY DIFFRACTION	f_chiral_restr	0.031	1079
X-RAY DIFFRACTION	f_plane_restr	0.004	1255

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 (%)
2.0401-2.0736	0.2706	138	0.2253	2361	X-RAY DIFFRACTION	90
2.0736-2.1093	0.2701	144	0.2176	2581	X-RAY DIFFRACTION	97
2.1093-2.1477	0.2611	140	0.202	2606	X-RAY DIFFRACTION	97
2.1477-2.189	0.2682	135	0.1976	2601	X-RAY DIFFRACTION	97
2.189-2.2336	0.2632	147	0.1969	2629	X-RAY DIFFRACTION	97
2.2336-2.2822	0.2414	127	0.1948	2543	X-RAY DIFFRACTION	98
2.2822-2.3353	0.2256	157	0.1851	2626	X-RAY DIFFRACTION	98
2.3353-2.3936	0.2368	127	0.1844	2592	X-RAY DIFFRACTION	98
2.3936-2.4583	0.2168	138	0.1816	2605	X-RAY DIFFRACTION	98
2.4583-2.5307	0.2274	137	0.1794	2629	X-RAY DIFFRACTION	98
2.5307-2.6123	0.2256	135	0.1785	2601	X-RAY DIFFRACTION	98
2.6123-2.7056	0.2325	146	0.1776	2646	X-RAY DIFFRACTION	98
2.7056-2.8139	0.2286	143	0.1871	2617	X-RAY DIFFRACTION	98
2.8139-2.9419	0.2376	134	0.1805	2621	X-RAY DIFFRACTION	98
2.9419-3.0969	0.2455	128	0.1768	2642	X-RAY DIFFRACTION	99
3.0969-3.2908	0.1944	128	0.1672	2642	X-RAY DIFFRACTION	99
3.2908-3.5446	0.2187	156	0.1597	2639	X-RAY DIFFRACTION	99
3.5446-3.9008	0.1993	140	0.1494	2627	X-RAY DIFFRACTION	99
3.9008-4.464	0.1712	153	0.1313	2662	X-RAY DIFFRACTION	99
4.464-5.6197	0.1638	152	0.1269	2600	X-RAY DIFFRACTION	99
5.6197-32.9692	0.1733	141	0.1625	2657	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	1.8103	-0.2077	-0.5065	4.5802	-0.0935	1.7277	-0.1869	-0.7157	0.1095	0.762	0.1287	0.2001	0.0421	0.7747	0.061	0.4833	0.0147	-0.0015	0.6012	-0.0273	0.2646	-13.5538	5.3449	5.5609
2	1.3454	0.7163	-0.7751	3.5874	0.7334	2.8374	-0.0994	-0.6228	-0.0052	-0.0093	-0.0591	-0.4563	0.1879	0.6878	0.1111	0.1964	0.064	-0.0333	0.503	0.0418	0.2374	-8.6901	4.3574	-2.8287
3	2.4364	-0.0444	-0.3537	3.5634	1.2208	2.0663	-0.0077	-0.5444	0.0175	0.2459	-0.17	-0.0844	0.2385	0.4263	0.1006	0.2192	0.0396	0.0297	0.3791	0.0108	0.2267	-15.4625	2.4711	-3.7776
4	0.1997	-0.1233	0.0394	0.2587	-0.021	-0.0426	-0.2913	-0.1607	0.2695	-0.5198	0.6191	-0.7249	-0.1628	0.1787	-0.3416	0.3412	-0.0778	0.032	0.3793	-0.1599	0.3578	-20.0232	21.9397	2.2822
5	3.8266	1.2468	-0.7477	2.8199	0.4346	1.5884	-0.0142	0.1807	0.3219	0.0759	-0.0312	0.0811	0.0803	-0.1224	0.0416	0.1994	-0.0117	-0.0195	0.275	-0.002	0.2157	-41.3917	32.1543	-1.3167
6	2.7141	-0.0065	0.8385	2.2665	0.4751	1.6073	-0.048	-0.3095	-0.2576	0.2744	0.0152	-0.0071	0.1892	0.0151	0.0152	0.2639	-0.0231	-0.021	0.2296	0.0229	0.2111	-39.4715	26.5335	2.5909
7	1.9931	0.1459	1.8043	1.9869	0.1849	6.6497	-0.2968	0.2583	0.1613	0.1203	0.1557	0.4541	-1.2612	-0.2502	0.1539	0.4097	0.0294	0.0301	0.3112	-0.0435	0.3392	-46.6748	35.6798	-1.8636
8	1.9514	-0.648	-0.6216	1.5627	-0.1291	1.3517	0.0295	0.0926	-0.0704	-0.2102	0.0257	0.1197	0.2438	-0.0622	-0.0478	0.2621	-0.019	0.0088	0.1798	0.027	0.215	-23.8354	-3.068	-19.6317
9	2.9627	0.3095	0.7033	2.9236	-0.4881	1.592	-0.0878	-0.2674	-0.3217	0.0084	0.0885	0.3293	0.1871	-0.1255	-0.032	0.2996	0.002	0.0659	0.2186	0.0341	0.2914	-27.413	-6.9861	-10.8415
10	1.7077	-1.3719	0.0868	1.1952	-0.1921	0.6242	-0.0824	-0.2673	-0.3195	-0.0044	0.0446	0.2762	0.2117	-0.0683	0.0442	0.2383	-0.0257	0.0418	0.235	0.0017	0.2914	-31.5643	1.906	-13.0046
11	1.2197	1.0122	0.2076	2.7825	-0.3707	1.4196	0.0918	-0.0427	0.1165	0.1107	-0.14	-0.0448	0.0569	0.0518	0.0524	0.1773	-0.014	0.0055	0.2241	-0.0048	0.2488	-41.3077	31.0034	-11.5097
12	0.9481	0.0545	0.2852	2.497	0.0137	0.992	0.0747	-0.0296	0.0009	0.1544	-0.2449	-0.2896	-0.1084	0.1131	0.145	0.1836	-0.0204	-0.0044	0.2503	0.0151	0.2417	-37.8849	29.3884	-12.9559
13	0.4602	-0.0731	-0.0705	1.6006	-0.7514	1.2537	-0.0153	-0.1966	0.092	-0.3098	-0.0564	0.2095	-0.4057	-0.1548	0.1758	0.2824	0.0375	-0.0389	0.349	-0.019	0.253	-48.0449	39.0742	-15.9197
14	3.6978	-0.4543	-0.4806	2.8487	0.1624	1.3148	0.2118	0.2713	0.429	-0.3637	-0.0601	-0.425	-0.248	0.0203	-0.1222	0.3904	0.0449	0.0936	0.2381	0.0258	0.2938	7.5119	-15.0426	-44.8071
15	3.2656	-0.0099	0.102	3.2548	1.2698	2.4433	0.1555	0.3564	0.1191	-0.2217	-0.2682	0.141	-0.024	-0.0866	0.0902	0.2015	0.0243	-0.0295	0.2817	0.0081	0.2107	21.2947	-48.3319	-48.6523
16	0.3133	0.4682	-0.4561	2.7128	-1.5614	6.1875	0.5236	0.025	-0.1056	-0.5272	0.024	0.0084	0.4357	0.369	-0.3213	0.4767	0.0522	-0.0225	0.2792	-0.0367	0.418	21.7845	-65.2839	-37.5691
17	1.2869	-0.6761	-0.2862	2.2459	0.5801	0.7922	0.039	-0.0066	-0.0722	0.1014	-0.055	0.1591	-0.0259	-0.1963	0.0317	0.1933	0.0133	-0.0135	0.2231	0.0149	0.2006	-6.392	-25.7351	-28.9097
18	2.878	-0.102	0.2087	3.5143	-0.9823	2.442	0.0825	-0.0443	-0.0333	-0.3709	-0.0203	0.2779	0.0532	-0.3062	-0.0248	0.2365	0.031	-0.047	0.2528	-0.0043	0.2195	-9.4865	-26.6623	-38.1898
19	0.5445	-0.9595	-0.2099	2.4401	-0.1978	-0.1124	0.0621	0.0814	-0.1598	-0.2635	-0.0515	0.377	-0.0146	-0.1407	-0.0285	0.2437	-0.0162	-0.0407	0.266	-0.0423	0.2597	-2.79	-33.6265	-35.7026
20	3.3385	0.4358	0.1217	0.9335	-0.4503	0.6081	0.0375	0.1392	-0.0147	0.0066	-0.0585	-0.0522	0.0209	-0.0565	0.0223	0.2222	-0.0348	-0.0116	0.1753	-0.0192	0.1891	20.7781	-52.8447	-35.7854
21	2.7626	-0.7275	0.2082	0.9925	-0.3218	1.6083	-0.0572	-0.1198	0.2263	0.019	-0.0441	0.0105	-0.0107	-0.0164	0.1015	0.2527	-0.0365	-0.0171	0.1933	-0.0304	0.2002	19.7882	-52.5615	-31.891
22	0.9462	-1.3233	-0.9618	2.0372	1.488	1.0843	-0.09	-0.9613	-0.0589	-1.3752	0.1892	-0.1172	0.3151	0.5921	0.0672	0.7843	0.0188	0.0881	0.5124	0.0993	0.3834	37.8048	-68.6317	-37.5803

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 33 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 34 through 82 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 82A through 103 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 104 through 119 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 120 through 147 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 148 through 215 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 216 through 242 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 0 through 32 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 33 through 75 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 76 through 113 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 114 through 150 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 151 through 188 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 189 through 224 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 1 through 111 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 112 through 225 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 226 through 243 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 1 through 32 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 33 through 75 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 76 through 113 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 114 through 150 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 151 through 210 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 211 through 224 )

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+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

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
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

-
Yorodumi