PDB-4m7z: Unliganded 1 crystal structure of S25-26 Fab

ID or keywords:

Entry

Database: PDB / ID: 4m7z

Title

Unliganded 1 crystal structure of S25-26 Fab

Components

(S25-26 Fab (Igg1k) ...) x 2

Keywords

IMMUNE SYSTEM / Beta-Sandwich / Carbohydrate/Sugar Binding

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.75 Å

Authors

Haji-Ghassemi, O. / Evans, S.V. / Muller-Loennies, S. / Saldova, R. / Muniyappa, M. / Brade, L. / Rudd, P.M. / Harvey, D.J. / Kosma, P. / Brade, H.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Groove-type Recognition of Chlamydiaceae-specific Lipopolysaccharide Antigen by a Family of Antibodies Possessing an Unusual Variable Heavy Chain N-Linked Glycan.
Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Saldova, R. / Muniyappa, M. / Brade, L. / Rudd, P.M. / Harvey, D.J. / Kosma, P. / Brade, H. / Evans, S.V.

History

Deposition	Aug 12, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 11, 2014	Group: Database references
Revision 1.2	Jul 9, 2014	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.4	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4m7z.cif.gz	347.1 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	4m7z.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m7/4m7z ftp://data.pdbj.org/pub/pdb/validation_reports/m7/4m7z	HTTPS FTP

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Related structure data

Related structure data	4m7jC 4m93C 4ma1C C: citing same article (ref.)
Similar structure data	5jor-3 4m93-2 5i1l-2 5waw-d 6p9i-1 4mhj-5 4why-4 5ywf-1 4yxl-2 4hxb-d 3qg6-1 5jor-4 3cfe-2 6co3-d 6c5i-d 1kem-d 3cmo-1 5vh3-1 4why-1 3cfd-1 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

Related structure data

4m7jC

4m93C

4ma1C

C: citing same article (ref.)

Similar structure data

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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

B: S25-26 Fab (Igg1k) Heavy Chain

H: S25-26 Fab (Igg1k) Heavy Chain

C: S25-26 Fab (Igg1k) Light Chain

L: S25-26 Fab (Igg1k) Light Chain

hetero molecules

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

1

B: S25-26 Fab (Igg1k) Heavy Chain

C: S25-26 Fab (Igg1k) Light Chain

hetero molecules

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

2

H: S25-26 Fab (Igg1k) Heavy Chain

L: S25-26 Fab (Igg1k) Light Chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.298, 111.988, 156.925
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	H
1	2	C
2	2	L

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	B	4 - 217
2	1	H	4 - 217
1	2	C	1 - 217
2	2	L	1 - 217

NCS ensembles :

ID
1
2

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Antibody , 2 types, 4 molecules BHCL

#1: Antibody	S25-26 Fab (Igg1k) Heavy Chain Mass: 23531.480 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/C
#2: Antibody	S25-26 Fab (Igg1k) Light Chain Mass: 24356.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/C

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Sugars , 1 types, 2 molecules

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 141 molecules

#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.91 Å³/Da / Density % sol: 68.56 %
Crystal grow	Temperature: 289 K / pH: 7.5 Details: 0.2M calcium chloride, 0.1M HEPES, 28% (v/v) PEG 400 , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 27, 2012 / Details: VERTICAL FOCUSING MIRROR
Radiation	Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.75→25 Å / Num. obs: 39918 / % possible obs: 100 % / Redundancy: 7.1 % / R_merge(I) obs: 0.087 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.75→2.85 Å / Redundancy: 7 % / R_merge(I) obs: 0.672 / % possible all: 99.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.75 Å	29.44 Å
Translation	2.75 Å	29.44 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.3.0	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→24.76 Å / Cor.coef. F_o:F_c: 0.943 / Cor.coef. F_o:F_c free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 22.987 / SU ML: 0.231 / SU R Cruickshank DPI: 0.5057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.506 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	1997	5 %	RANDOM
R_work	0.216	-	-	-
obs	0.217	39858	99.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 52.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.39 Å²	0 Å²	0 Å²
2-	-	6.97 Å²	0 Å²
3-	-	-	-3.59 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→24.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6672	0	177	124	6973

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.02	7014
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	6492
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.963	9503
X-RAY DIFFRACTION	r_angle_other_deg	3.663	3.002	15006
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.799	5	864
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.266	23.978	269
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.861	15	1084
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.692	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	1058
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	7758
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1562
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0	2	3468
X-RAY DIFFRACTION	r_mcbond_other	0	2	3467
X-RAY DIFFRACTION	r_mcangle_it	0	3	4328
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	B	11482	0.11
1	2	H	11482	0.11
2	1	C	11726	0.13
2	2	L	11726	0.13

LS refinement shell

Resolution: 2.75→2.82 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	146	-
R_work	0.338	2766	-
obs	-	-	99.69 %

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	3.0077	-0.8472	2.9878	3.6599	-0.6336	3.2593	-0.0921	-0.0534	0.1721	0.0382	0.0878	0.1415	-0.1489	-0.2173	0.0043	0.0946	0.0202	0.0458	0.139	0.0889	0.1296	55.6762	-10.0341	-13.8901
2	5.2922	-1.8426	1.1454	3.4802	-1.1179	3.0048	0.0678	0.0891	0.1961	0.1685	-0.0235	0.1825	-0.1485	-0.0523	-0.0443	0.3379	-0.0352	0.0561	0.1492	0.0332	0.1264	38.0219	15.5329	-32.3935
3	7.0015	-1.3556	0.8854	2.8375	-1.2995	2.8389	-0.0259	-0.0533	0.5719	0.2326	0.0017	0.0885	-0.503	-0.064	0.0242	0.3978	-0.0034	0.0561	0.1492	0.0286	0.1518	35.8431	16.8478	-31.3387
4	4.987	2.7827	0.9012	3.313	0.1332	3.6598	-0.0264	0.4365	0.3491	-0.1982	-0.0335	-0.2487	-0.2729	0.2285	0.0599	0.1274	0.0045	0.0406	0.1374	0.0904	0.1426	-8.5911	-5.7895	-6.6102
5	6.7823	1.953	-0.1048	4.3125	-1.1708	2.1005	0.2634	-0.0677	0.9696	0.2027	0.3142	0.2822	-0.4398	-0.3626	-0.5776	0.5849	0.1214	0.286	0.5605	0.2113	0.6124	8.6262	23.919	-18.1249
6	5.4388	-0.5496	0.2623	3.8163	-0.2763	4.0618	0.2447	0.2776	1.0176	-0.3408	0.2415	0.1325	-0.811	-0.7052	-0.4861	0.6596	0.1211	0.3094	0.4455	0.1826	0.673	10.799	23.4123	-19.9828
7	4.9883	-1.58	0.6713	3.6769	-1.279	1.8425	-0.0385	0.2024	0.0896	-0.077	0.2276	0.2696	-0.066	-0.3014	-0.1891	0.1499	-0.0397	0.0203	0.104	0.0553	0.0538	37.6543	-20.7174	-17.7696
8	11.0401	2.4343	13.531	12.4977	-5.2665	22.2758	0.3	0.6078	-0.513	0.2604	0.7571	0.5505	0.1719	0.3378	-1.0571	0.2	0.0192	0.0658	0.5655	0.2605	0.3169	21.5234	-8.1354	-27.6945
9	3.8739	1.9055	-2.6062	3.2392	-3.653	7.3271	0.049	-0.0419	-0.204	-0.1155	-0.024	-0.0096	0.2511	0.1195	-0.025	0.2131	0.0575	-0.0281	0.1215	0.0843	0.147	35.1281	4.9997	-42.8443
10	4.0458	1.0101	-1.2493	3.3933	-1.163	3.5333	-0.0015	-0.0255	0.2531	-0.1691	0.0109	-0.3978	-0.2131	0.404	-0.0095	0.1456	0.0017	-0.0187	0.1278	-0.0086	0.1116	9.5741	-8.404	4.0923
11	18.4992	15.6291	5.3987	33.6066	2.6506	1.7812	0.3511	-0.6399	0.2608	0.6491	-0.4193	-0.8089	-0.0044	-0.2048	0.0682	0.41	-0.1597	0.1257	0.4452	0.1331	0.5371	25.1876	7.4976	-0.737
12	5.2171	-2.9353	1.1249	7.6688	-1.6772	3.649	0.1364	-0.5275	1.0404	1.001	0.1649	0.075	-1.25	-0.6125	-0.3013	0.9094	0.0317	0.3661	0.6509	-0.0886	0.825	11.6901	27.5254	-3.8919

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	4 - 116
2	X-RAY DIFFRACTION	2	B	117 - 164
3	X-RAY DIFFRACTION	3	B	165 - 214
4	X-RAY DIFFRACTION	4	H	4 - 116
5	X-RAY DIFFRACTION	5	H	117 - 164
6	X-RAY DIFFRACTION	6	H	165 - 213
7	X-RAY DIFFRACTION	7	C	1 - 109
8	X-RAY DIFFRACTION	8	C	110 - 115
9	X-RAY DIFFRACTION	9	C	116 - 214
10	X-RAY DIFFRACTION	10	L	1 - 109
11	X-RAY DIFFRACTION	11	L	110 - 115
12	X-RAY DIFFRACTION	12	L	116 - 213

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