PDB-7c95: Crystal structure of the anti-human podoplanin antibody Fab fragment

ID or keywords:

Entry

Database: PDB / ID: 7c95

Title

Crystal structure of the anti-human podoplanin antibody Fab fragment

Components

Heavy chain of Fab fragment
Light chain of Fab fragment

Keywords

IMMUNE SYSTEM / human podoplanin / monoclonal antibody / glycopeptide

Function / homology

TRIETHYLENE GLYCOL

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.13 Å

Authors

Nakamura, S. / Suzuki, K. / Ogasawara, S. / Naruchi, K. / Shimabukuro, J. / Tukahara, N. / Kaneko, M.K. / Kato, Y. / Murata, T.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of an anti-podoplanin antibody bound to a disialylated O-linked glycopeptide.
Authors: Ogasawara, S. / Suzuki, K. / Naruchi, K. / Nakamura, S. / Shimabukuro, J. / Tsukahara, N. / Kaneko, M.K. / Kato, Y. / Murata, T.

History

Deposition	Jun 4, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 4, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 29, 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 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7c95.cif.gz	422.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7c95.ent.gz	290 KB	Display	PDB format
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Validation report

Summary document	7c95_validation.pdf.gz	489.6 KB	Display	wwPDB validaton report
Full document	7c95_full_validation.pdf.gz	500.4 KB	Display
Data in XML	7c95_validation.xml.gz	33.4 KB	Display
Data in CIF	7c95_validation.cif.gz	45.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/7c95 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/7c95	HTTPS FTP

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Related structure data

Related structure data	7c94C 1a3lS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5vh4-2 6dwc-2 6nov-2 4jn1-d 5mp1-2 3i2c-d 1rz8-1 6w5a-d 6cdp-d 1fl6-1 5mu2-7 1mjj-1 5mu0-3 4hdi-1 5ijk-1 3bz4-3 5a16-3 1bbd-d 4ojf-d 5mu2-1 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

7c94C

1a3lS

S: Starting model for refinement

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

C: Light chain of Fab fragment

D: Heavy chain of Fab fragment

A: Light chain of Fab fragment

B: Heavy chain of Fab fragment

hetero molecules

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

1

C: Light chain of Fab fragment

D: Heavy chain of Fab fragment

hetero molecules

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

2

A: Light chain of Fab fragment

B: Heavy chain of Fab fragment

hetero molecules

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

Unit cell

Length a, b, c (Å)	53.720, 65.850, 117.750
Angle α, β, γ (deg.)	90.000, 97.274, 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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Antibody , 2 types, 4 molecules CADB

#1: Antibody	Light chain of Fab fragment Mass: 24260.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody	Heavy chain of Fab fragment Mass: 24145.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 4 types, 149 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.13 Å³/Da / Density % sol: 42.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Tris-HCl, 0.2M magnesium Acetate, 25% v/v PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-1A / Wavelength: 1.1 Å

Detector

Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 28, 2018

Radiation

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

Radiation wavelength

Wavelength: 1.1 Å / Relative weight: 1

Reflection

Resolution: 2.13→46.32 Å / Num. obs: 44820 / % possible obs: 97.7 % / Redundancy: 11.668 % / B_iso Wilson estimate: 36.58 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.097 / Net I/σ(I): 17.3

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	Diffraction-ID	% possible all
2.13-2.26	0.639	2.15	6701	0.878	1	90.4
2.26-2.41	0.593	3.78	6590	0.939	1	98.8
2.41-2.61	0.384	6.2	6606	0.979	1	98.6
2.61-2.85	0.237	10.36	5725	0.992	1	98.8
2.85-3.19	0.139	16.75	5428	0.996	1	99.3
3.19-3.68	0.085	27.36	4762	0.998	1	99.6
3.68-4.5	0.055	41.1	4043	0.998	1	99.5
4.5-6.34	0.047	48.83	3140	0.999	1	99.9
6.34-46.32	0.039	52.04	1825	0.999	1	99.7

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	1.14	refinement
PDB_EXTRACT	3.25	data extraction
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1A3L

1a3l

Resolution: 2.13→46.32 Å / SU ML: 0.3022 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.259 / Stereochemistry target values: CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2374	2241	5 %
R_work	0.204	42553	-
obs	0.2057	44794	97.7 %

Solvent computation

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

Displacement parameters

B_iso mean: 48.75 Å²

Refinement step

Cycle: LAST / Resolution: 2.13→46.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6654	0	103	131	6888

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0027	6958
X-RAY DIFFRACTION	f_angle_d	0.6066	9476
X-RAY DIFFRACTION	f_chiral_restr	0.0423	1051
X-RAY DIFFRACTION	f_plane_restr	0.004	1198
X-RAY DIFFRACTION	f_dihedral_angle_d	15.4342	4133

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 (%)
2.13-2.18	0.3949	122	0.3388	2323	X-RAY DIFFRACTION	85.43
2.18-2.23	0.3489	128	0.3099	2431	X-RAY DIFFRACTION	90.78
2.23-2.28	0.3089	140	0.2881	2668	X-RAY DIFFRACTION	98.63
2.28-2.34	0.336	139	0.2925	2634	X-RAY DIFFRACTION	97.5
2.34-2.41	0.3008	142	0.2632	2694	X-RAY DIFFRACTION	99.47
2.41-2.49	0.3129	141	0.264	2672	X-RAY DIFFRACTION	98.39
2.49-2.58	0.3171	140	0.2575	2668	X-RAY DIFFRACTION	98.39
2.58-2.68	0.3014	142	0.2636	2691	X-RAY DIFFRACTION	98.85
2.68-2.81	0.2848	142	0.253	2691	X-RAY DIFFRACTION	99.47
2.81-2.95	0.2629	141	0.2334	2677	X-RAY DIFFRACTION	99.09
2.95-3.14	0.2429	143	0.2206	2712	X-RAY DIFFRACTION	99.24
3.14-3.38	0.2703	141	0.2146	2679	X-RAY DIFFRACTION	99.09
3.38-3.72	0.208	143	0.1862	2719	X-RAY DIFFRACTION	99.76
3.72-4.26	0.2255	144	0.1599	2732	X-RAY DIFFRACTION	99.58
4.26-5.36	0.1576	145	0.1341	2760	X-RAY DIFFRACTION	99.73
5.36-46.32	0.1751	148	0.1723	2802	X-RAY DIFFRACTION	99.76

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	7.83624090313	1.87642520187	-0.00787728568439	4.73275920203	1.40916387768	3.91642595266	0.268394670907	-0.936808795297	0.668447081484	0.522486850509	-0.26865871701	0.102552522646	0.106430846798	0.189423444346	-0.0351513345426	0.268560050508	-0.0356880247659	-0.0193543743472	0.399652718126	-0.0774685193263	0.31972298949	8.96331357232	21.0295656437	75.6874240194
2	3.67028598067	-0.313239569767	1.13999362738	0.692084943995	0.288079586163	8.02219451187	-0.0236508363285	-0.0417650180793	0.173832080455	0.0500077358091	-0.056594711931	-0.0134422026463	-0.350830558001	-0.183075406713	0.0996769281313	0.165579970577	-0.0154392151471	0.00123046689069	0.170803642592	-0.0224755508628	0.271025912584	13.0109708807	21.1532931043	42.6380853341
3	7.73564666876	-0.838091912938	0.607648423846	1.66708994707	-0.232098281524	7.49714988777	0.047300366836	0.578022766908	0.510506553251	-0.0552353796421	0.00556101672551	-0.119071708923	-0.527335017035	0.0616734384574	-0.0237031053461	0.198204562691	-0.00366259353322	0.0308035211981	0.24468608787	0.0303292341003	0.331251104065	12.7413615836	23.7368568837	30.7954598429
4	5.55255513914	-1.76752428125	1.23784574262	3.76206510705	-3.21710859497	9.39209475613	-0.166462700604	-0.310299896075	-1.0028453629	0.0555338974754	0.0836273723087	0.16842026641	0.911445534689	-0.288777740537	0.0568181807947	0.323607978914	-0.0490312201708	0.0549782893977	0.220008183118	-0.0182053526942	0.447133228523	-11.2508895126	7.59832352001	67.9645982144
5	2.67169153888	-2.17546206795	-2.17759322534	4.93528596751	2.77066705082	4.94234211149	0.0664522135773	0.154268404906	0.518708956227	-0.0239004697505	0.0155879838023	-0.653908750881	-0.392408944116	0.282621559517	-0.222523315376	0.220371398324	0.02064484461	-0.0279710770531	0.317438638808	0.0154586122769	0.379508650256	-6.57265679184	19.7903837135	68.5804139696
6	7.46025425113	3.23846245387	-0.497790478849	5.93057842292	-2.43687289136	9.65284820332	-0.185755737773	-1.86449462774	0.0808598155363	0.441694929943	-0.166305532059	0.526428224437	-0.202262820303	-0.088470889867	0.335080137159	0.35080079028	0.158671658456	0.0651579153198	0.57833490148	0.00867127140187	0.399309019246	-16.1469908181	17.9718983336	78.0530399458
7	2.73327652689	-2.30762697477	1.17986429714	6.46692181449	-2.4121443033	6.63147750225	0.0362339618667	-0.359537020802	-0.532543166959	-0.0249449801022	-0.146385817774	0.476441738195	0.818240376914	-0.893018818152	0.0167783335125	0.326645486715	-0.0644366805077	0.0196790137203	0.312703899399	-0.00228783611755	0.497281565604	-17.4667890787	10.7592238802	71.2051517022
8	7.90677385819	-4.38014175448	4.77159798828	8.94028950993	-5.77113275412	4.22619924276	-0.175359677609	0.167060994625	0.262204567259	0.114738686773	-0.111607582416	-0.118196964069	-0.115258909642	0.0627309299899	0.195694220306	0.192245684062	-0.00517203788596	-0.00712551400335	0.25722885531	-0.0271667934392	0.198394305787	-10.8071678318	18.21959642	63.780804701
9	5.11816365886	-0.879868356475	-0.0784522279089	5.09652202971	-0.0758770494918	-0.011856386057	0.274839351605	-0.925728083983	-0.371960559669	0.884281782612	0.0674235103705	0.309459552417	0.148177719995	-0.349714206558	-0.206493964461	0.356922009014	-0.0337240120605	0.0961147965798	0.460691697044	0.0339593064263	0.23889905558	-4.7675750795	13.1558894169	73.3711717635
10	1.84711887351	-2.28848066504	0.496721274551	4.67741029121	1.50196149765	4.64203577465	0.138214805012	0.890044682059	-0.240357850992	-0.334800238774	-0.237177496059	0.050814139415	-0.115418705258	-0.282640309877	0.075553404188	0.181738782565	-0.065762557768	-0.015109783425	0.274491842969	0.0171407245728	0.191453874027	-1.78093873147	12.6781043066	38.8864178291
11	7.63098239572	-1.97206261781	-2.33172257165	2.57536903443	0.444914396045	4.74334015783	0.124397273682	-0.35956211251	-0.45808331296	0.100376289628	-0.0248799621674	0.0573871081062	0.292595848512	-0.298761524408	-0.0829149284715	0.165678259498	-0.0874885105093	-0.0389305666707	0.256492127524	-0.00904623307378	0.320139981277	3.09172316511	9.50141242178	43.7288621183
12	7.88846175435	-0.370105743985	-2.84387605113	2.05517205565	3.60730943241	7.5739144529	-0.00243371800506	-0.292308839652	0.177977659548	0.00809186375808	0.0567497857309	-0.211918686959	-0.0808439799991	-0.210127333131	-0.144444766285	0.147336667157	-0.051393412867	0.0120063691528	0.163845808628	0.0185334688597	0.250024791686	5.71479722028	13.3905826447	44.9475765688
13	6.90813715741	-4.43368349298	-4.04879874642	2.7068243366	2.2688147061	5.02740164681	0.191106135132	0.255533912725	-1.16402535462	-0.301679348633	-0.196782753462	0.176988894793	0.16715273853	-0.281385042378	0.0558486483554	0.328702658912	-0.0861702786585	-0.0188407145959	0.29259080689	-0.0819703745756	0.556209679956	4.86734560256	2.83725148515	38.3864044109
14	3.57372903708	0.213096090625	0.513207843459	2.16155468678	0.175424354826	6.2920530532	0.0900021289239	0.0070487308634	-0.121400380541	0.018848548536	0.0314622566874	0.205134256778	0.976484305162	-0.798075305809	-0.0826831694562	0.564659888605	-0.0765987076523	-0.0486589162345	0.345443154988	0.0272501669887	0.264781626593	-19.8157726389	19.0415293666	-18.2872636256
15	0.973599358795	-0.182709650466	-2.14582788705	0.353950139437	-0.209902180536	7.02475145397	0.0675344464777	0.117507036879	0.118046166248	-0.137453794601	0.052487199414	0.0347007184512	-0.0361733564427	-0.292644883726	-0.116367147295	0.250731268557	-0.040305337868	-0.0232758113865	0.27470519465	0.0284882683106	0.296428010886	-21.2413742643	20.5111501998	7.32662397545
16	3.71886881822	0.61786876528	0.31109162198	1.17769656083	0.826861123551	9.18256206859	-0.0448654594654	0.136766246704	0.377612204666	-0.150850922542	0.129659406503	0.159180848233	-0.597684214762	-0.253925412646	-0.0398008541147	0.235471008738	0.0121349066529	0.00329393231165	0.216654917251	0.0713813036423	0.336329554689	-25.1485602209	24.8273719121	21.4075941029
17	3.45220990101	0.956564338922	0.384480316661	2.81566848149	0.976649711837	5.78838996008	0.0553206843435	-0.105682577805	-0.255023725906	-0.266578763636	0.0635825367859	-0.333555765319	-0.0517599926603	0.658158358271	-0.114873798058	0.341753329095	0.0503853587063	-0.0233781692342	0.424292224061	0.0232636683856	0.261818974197	0.899853709311	14.0959377821	-10.5584089001
18	4.83735889095	1.09218762995	1.37278993343	4.20320907373	1.73249532413	1.07433735299	0.0233086631434	0.203263004575	-0.193664728782	-0.704679094523	0.0402892910646	-0.174623110547	-0.475793553949	0.445124014019	-0.0732019285176	0.550746340219	-0.0046497960624	0.00168071733176	0.484312370677	0.0491737280995	0.247076107675	1.59319042904	15.8251538468	-11.2412206752
19	7.17678404508	5.90823751816	-6.94814074104	6.84050772759	-4.11377746482	8.90002539629	-0.0242657600908	-0.36925071805	0.564282341848	0.0950215209731	0.11879761529	0.500887925796	0.170316298	0.514496043059	-0.0717164307369	0.240069175743	0.141850317071	-0.0286317475017	0.430759589124	-0.00644459135048	0.263770440275	-11.8556762145	16.0359753133	18.0673551708
20	6.8361473404	0.244724490897	-2.50519817818	2.63824157226	0.235136984729	6.381213716	-0.491749109206	-0.398816767773	-0.657685470149	0.205303508308	0.162795283374	0.0957021760294	1.07854793385	0.571831057306	0.290649674493	0.452792750781	0.116622084292	0.0825504753857	0.328458688988	0.0672103836335	0.274961474208	-13.7185365882	10.4949424795	16.7364911036

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 1 through 107 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 108 through 180 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 181 through 219 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 1 through 33 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 34 through 51 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 52 through 64 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 65 through 83 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 84 through 98 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 99 through 120 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 121 through 143 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 144 through 166 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 167 through 193 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 194 through 222 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 1 through 96 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 97 through 150 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 151 through 220 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 1 through 60 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 61 through 118 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 119 through 154 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 155 through 224 )

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