PDB-9b74: Crystal structure of humanized 44H10 Fab Version 14

ID or keywords:

Entry

Database: PDB / ID: 9b74

Title

Crystal structure of humanized 44H10 Fab Version 14

Components

(h44H10-V14 Antibody, ...) x 2

Keywords

IMMUNE SYSTEM / Antibody / Humanized

Function / homology

ACETATE ION

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.48 Å

Authors

Kassardjian, A. / Julien, J.P.

Funding support

Canada, 1items

Citation

Journal: Antibodies / Year: 2024
Title: Humanization of Pan-HLA-DR mAb 44H10 Hinges on Critical Residues in the Antibody Framework.
Authors: Kassardjian, A. / Ivanochko, D. / Barber, B. / Jetha, A. / Julien, J.P.

History

Deposition	Mar 27, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 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	9b74.cif.gz	220.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9b74_validation.pdf.gz	449.1 KB	Display	wwPDB validaton report
Full document	9b74_full_validation.pdf.gz	449.7 KB	Display
Data in XML	9b74_validation.xml.gz	19.4 KB	Display
Data in CIF	9b74_validation.cif.gz	28 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b7/9b74 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/9b74	HTTPS FTP

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Related structure data

Related structure data	9b75C 9b76C 9b7bC C: citing same article (ref.)
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: h44H10-V14 Antibody, heavy chain

L: h44H10-V14 Antibody, light chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	123.325, 123.325, 90.714
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

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Antibody , 2 types, 2 molecules HL

#1: Antibody	h44H10-V14 Antibody, heavy chain Mass: 23555.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody	h44H10-V14 Antibody, light chain Mass: 23351.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 225 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 207 / 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: 4.25 Å³/Da / Density % sol: 71.03 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 15% glycerol, 25.5% PEG4000, 0.17 M sodium acetate, 0.085 M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.48→40 Å / Num. obs: 28548 / % possible obs: 99.8 % / Redundancy: 3.9 % / B_iso Wilson estimate: 36.19 Å² / CC_1/2: 0.977 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.48→2.52 Å / Num. unique obs: 1351 / CC_1/2: 0.506

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.48→36.88 Å / SU ML: 0.2717 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2052	1433	5.03 %
R_work	0.1744	27082	-
obs	0.1759	28515	99.77 %

Solvent computation

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

Displacement parameters

B_iso mean: 39.62 Å²

Refinement step

Cycle: LAST / Resolution: 2.48→36.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3298	0	51	207	3556

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0066	3416
X-RAY DIFFRACTION	f_angle_d	0.8733	4640
X-RAY DIFFRACTION	f_chiral_restr	0.0509	534
X-RAY DIFFRACTION	f_plane_restr	0.0052	588
X-RAY DIFFRACTION	f_dihedral_angle_d	13.2236	1214

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 (%)
2.48-2.57	0.3276	143	0.2796	2682	X-RAY DIFFRACTION	99.72
2.57-2.67	0.3	142	0.257	2687	X-RAY DIFFRACTION	99.79
2.67-2.79	0.2504	143	0.2542	2659	X-RAY DIFFRACTION	99.89
2.79-2.94	0.2939	138	0.2363	2701	X-RAY DIFFRACTION	99.79
2.94-3.12	0.2432	145	0.2068	2675	X-RAY DIFFRACTION	99.86
3.12-3.36	0.2524	143	0.1799	2697	X-RAY DIFFRACTION	99.86
3.37-3.7	0.1904	143	0.1638	2678	X-RAY DIFFRACTION	99.75
3.7-4.24	0.1738	148	0.132	2739	X-RAY DIFFRACTION	99.86
4.24-5.34	0.1397	140	0.1192	2746	X-RAY DIFFRACTION	99.9
5.34-36.88	0.152	148	0.1598	2818	X-RAY DIFFRACTION	99.3

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	2.13161222713	0.459058460887	3.28725968057	0.784180077132	0.873516544961	6.42789593276	0.180880231325	0.275429388185	-0.340680671188	-0.0627347088144	0.161292224733	-0.551868021012	0.388373148783	0.863063438563	-0.233842004036	0.34208731862	0.0251701134329	0.00957299156197	0.358685515963	-0.0493387111819	0.368026284792	-39.975	15.267	-1.599
2	2.08155974288	-0.37494747701	0.555953598202	1.47992961024	0.886215682049	2.66499176654	0.134281597118	-0.0015520305932	-0.354033660325	0.289229513456	0.341998555112	-0.192391259976	0.128267871269	0.874307583953	-0.388534081627	0.394861773994	0.0290197552064	-0.114116972721	0.431901592834	-0.0307370265562	0.513231970372	-35.697	9.659	10.004
3	5.24024361741	-0.372673422228	-0.698343386016	4.83227020109	0.592839908982	4.94353446357	0.383882944901	0.323111063014	-0.056067867686	-0.356956946221	-0.0557319028806	0.124724341652	-0.221092172569	-0.178193939333	-0.235290991273	0.235240822074	0.0132116691749	0.0165782716204	0.221224136385	4.94250283605E-5	0.288437707643	-49.534	15.232	4.912
4	2.87273011216	1.1463792884	-0.14525286223	2.29567816615	0.512709496878	2.37123665133	-0.0183087013944	-0.0285531023812	-0.541843840344	0.237933244497	0.0271957050497	-0.157077040285	0.21950996325	0.312533407572	0.0591193728749	0.422432268792	0.00831061442879	-0.0403482035505	0.212968492272	0.0148045797694	0.330054169202	-46.193	3.835	5.55
5	1.68385271751	0.615835397181	-0.471655723059	4.18282424341	-0.518569154899	1.24157243786	0.0708728654858	-0.174565640937	-0.359631461149	0.152376364764	-0.0631271078616	-0.210189729776	0.302671941849	0.287611776147	-0.0319960519729	0.26892058937	0.0132904361411	-0.0273482605913	0.315666199916	-0.0193025957953	0.308887669422	-44.196	9.892	4.393
6	1.50018766435	-0.336932479825	-0.0218347667285	4.30704035953	-3.1102988725	2.31601567335	-0.22737581788	-0.23161561352	-0.088785749579	0.617437182694	-0.124259613065	-0.229978748472	-0.0708836782877	-0.122316965979	0.365452696404	0.350512921149	-0.0246000734151	-0.0387231277256	0.203164124736	-0.0242881625248	0.301602351634	-45.858	15.369	5.709
7	1.05218881186	0.576104690346	0.0643110167906	4.47212778602	-0.415913109759	0.673589564943	0.130352801619	-0.024505961826	-0.0264025979405	0.288417478813	-0.114816011183	-0.440416375481	0.00891095928439	0.142867260813	-0.0165042138992	0.179730420268	-0.0492943227306	-0.017593451103	0.272906920882	-0.0285984604293	0.225029966172	-40.787	40.515	-3.957
8	1.60909664974	1.44732258182	0.907242220368	5.18278487202	1.46346401012	2.91820014389	0.106819662444	-0.214890461813	0.0886644419216	0.301212336102	-0.172373544254	-0.316674994929	-0.188422334828	0.140465612459	0.0954131642757	0.222238416325	-0.0418645157602	-0.0110034306461	0.23992802237	0.000915674718467	0.218225023176	-37.922	44.352	-2.365
9	6.59109432589	4.15933663679	3.91294856891	3.91235897812	4.59288424563	5.826028191	0.495207250216	0.629783143126	-1.29095433797	0.439083807496	0.574788980675	-2.07314124616	0.572931404215	0.998819013342	-0.662457991233	0.270125723743	0.0349254675392	-0.0281302993653	0.458360596173	-0.0868195514155	0.640311185501	-33.878	30.959	-7.582
10	1.04683024547	-1.4176164658	1.04568408171	2.21544310929	-0.53438653494	3.71568323126	0.461940193187	0.202863950985	0.259050108305	-0.514737070505	-0.427943442413	-1.03044638825	-0.176757166524	0.342277718668	8.21999009921E-6	0.253147059614	-0.0241859267744	0.0109910696813	0.400877123626	0.0263884257705	0.441134429449	-33.941	53.118	-7.333
11	1.47127114673	-1.05994209989	-0.596147356577	4.59647583249	-0.0785162414249	2.58956231556	-0.0684308557656	-0.0622271384481	-0.05254653061	0.804675354161	0.0538928100728	0.472093913496	0.305314984188	-0.23465872685	0.00637151393951	0.401173020399	-0.032652809899	0.0494556727707	0.237980631288	0.0112281463233	0.232528193658	-56.274	20.836	19.492
12	1.24249798066	0.06191773478	-0.792404056192	2.38959455562	-0.993267578239	4.67079113888	-0.0153355323504	0.205749853325	0.000957819736609	-0.10570458424	0.0204481475536	0.111253572207	-0.19286326474	-0.11541443273	-0.0318351961097	0.172362125513	-0.025392919552	-0.00966550648418	0.20176857872	-0.00826741814055	0.194893106292	-51.955	48.943	-4.341

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN H AND RESID 1:17 )	H	1 - 17
2	X-RAY DIFFRACTION	2	( CHAIN H AND RESID 18:32 )	H	18 - 32
3	X-RAY DIFFRACTION	3	( CHAIN H AND RESID 33:44 )	H	33 - 44
4	X-RAY DIFFRACTION	4	( CHAIN H AND RESID 45:74 )	H	45 - 74
5	X-RAY DIFFRACTION	5	( CHAIN H AND RESID 75:99 )	H	75 - 99
6	X-RAY DIFFRACTION	6	( CHAIN H AND RESID 100:115 )	H	100 - 115
7	X-RAY DIFFRACTION	7	( CHAIN H AND RESID 116:171 )	H	116 - 171
8	X-RAY DIFFRACTION	8	( CHAIN H AND RESID 172:196 )	H	172 - 196
9	X-RAY DIFFRACTION	9	( CHAIN H AND RESID 197:209 )	H	197 - 209
10	X-RAY DIFFRACTION	10	( CHAIN H AND RESID 210:216 )	H	210 - 216
11	X-RAY DIFFRACTION	11	( CHAIN L AND RESID 1:101 )	L	1 - 101
12	X-RAY DIFFRACTION	12	( CHAIN L AND RESID 102:214 )	L	102 - 214

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