PDB-4lri: Anti CMV Fab Fragment

ID or keywords:

Entry

Database: PDB / ID: 4lri

Title

Anti CMV Fab Fragment

Components

MSL-109 Heavy Chain
MSL-109 Light Chain

Keywords

IMMUNE SYSTEM / Fab Fragment / CMV neutralizing antibody / glycoprotein H or gH from CMV

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: 1.65 Å

Authors

Stengel, K.F.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Mechanism for neutralizing activity by the anti-CMV gH/gL monoclonal antibody MSL-109.
Authors: Fouts, A.E. / Comps-Agrar, L. / Stengel, K.F. / Ellerman, D. / Schoeffler, A.J. / Warming, S. / Eaton, D.L. / Feierbach, B.

History

Deposition	Jul 19, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 21, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 2, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4lri.cif.gz	186.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4lri.ent.gz	154.9 KB	Display	PDB format
PDBx/mmJSON format	4lri.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4lri_validation.pdf.gz	445.5 KB	Display	wwPDB validaton report
Full document	4lri_full_validation.pdf.gz	451.1 KB	Display
Data in XML	4lri_validation.xml.gz	38.8 KB	Display
Data in CIF	4lri_validation.cif.gz	57.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lr/4lri ftp://data.pdbj.org/pub/pdb/validation_reports/lr/4lri	HTTPS FTP

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Related structure data

Similar structure data	5alb-d 6bzu-4 3tcl-2 4xcy-2 4gxv-1 5dd1-d 5fhb-d 4nrz-2 2f5a-d 4ydv-2 2aab-d 1nc2-1 5nb5-2 3mnv-1 4qhl-1 6axl-2 6okq-3 3cmo-1 5mu2-6 6dg2-1 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

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

A: MSL-109 Light Chain

B: MSL-109 Light Chain

P: MSL-109 Heavy Chain

C: MSL-109 Heavy Chain

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

1

A: MSL-109 Light Chain

P: MSL-109 Heavy Chain

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

2

B: MSL-109 Light Chain

C: MSL-109 Heavy Chain

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

Unit cell

Length a, b, c (Å)	73.619, 101.649, 113.794
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	MSL-109 Light Chain Mass: 24006.762 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	MSL-109 Heavy Chain Mass: 24896.662 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.: 709 / 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: 2.18 Å³/Da / Density % sol: 43.49 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1mM Hepes pH 7.5, 70% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.65→40 Å / Num. obs: 102913 / % possible obs: 100 %

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→29.112 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2125	5147	5 %
R_work	0.187	-	-
obs	0.1883	102913	99.83 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 27.261 Å² / k_sol: 0.316 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.9132 Å²	0 Å²	-0 Å²
2-	-	3.3272 Å²	-0 Å²
3-	-	-	-2.4141 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→29.112 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6698	0	0	709	7407

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6861
X-RAY DIFFRACTION	f_angle_d	1.167	9321
X-RAY DIFFRACTION	f_dihedral_angle_d	12.921	2447
X-RAY DIFFRACTION	f_chiral_restr	0.084	1049
X-RAY DIFFRACTION	f_plane_restr	0.005	1193

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 (%)
1.65-1.6691	0.2537	161	0.23	3097	X-RAY DIFFRACTION	96
1.6691-1.6887	0.2541	168	0.2213	3205	X-RAY DIFFRACTION	100
1.6887-1.7093	0.2779	177	0.2144	3238	X-RAY DIFFRACTION	100
1.7093-1.7309	0.2662	157	0.2091	3217	X-RAY DIFFRACTION	100
1.7309-1.7537	0.2445	174	0.2049	3270	X-RAY DIFFRACTION	100
1.7537-1.7777	0.2375	158	0.1965	3194	X-RAY DIFFRACTION	100
1.7777-1.8031	0.2538	179	0.2004	3244	X-RAY DIFFRACTION	100
1.8031-1.83	0.2357	171	0.1962	3214	X-RAY DIFFRACTION	100
1.83-1.8586	0.2396	174	0.1957	3218	X-RAY DIFFRACTION	100
1.8586-1.8891	0.2387	199	0.189	3217	X-RAY DIFFRACTION	100
1.8891-1.9216	0.247	183	0.1952	3203	X-RAY DIFFRACTION	100
1.9216-1.9566	0.2271	162	0.1883	3282	X-RAY DIFFRACTION	100
1.9566-1.9942	0.2066	177	0.1942	3251	X-RAY DIFFRACTION	100
1.9942-2.0349	0.2588	164	0.1919	3233	X-RAY DIFFRACTION	100
2.0349-2.0791	0.2139	156	0.192	3251	X-RAY DIFFRACTION	100
2.0791-2.1275	0.2004	155	0.1885	3257	X-RAY DIFFRACTION	100
2.1275-2.1807	0.2281	189	0.1901	3224	X-RAY DIFFRACTION	100
2.1807-2.2396	0.2257	182	0.1903	3260	X-RAY DIFFRACTION	100
2.2396-2.3055	0.2438	164	0.1992	3258	X-RAY DIFFRACTION	100
2.3055-2.3799	0.2329	179	0.2021	3260	X-RAY DIFFRACTION	100
2.3799-2.4649	0.2602	175	0.2093	3251	X-RAY DIFFRACTION	100
2.4649-2.5635	0.2596	171	0.211	3260	X-RAY DIFFRACTION	100
2.5635-2.6801	0.2468	201	0.2115	3248	X-RAY DIFFRACTION	100
2.6801-2.8213	0.2349	174	0.2118	3272	X-RAY DIFFRACTION	100
2.8213-2.9979	0.216	160	0.206	3294	X-RAY DIFFRACTION	100
2.9979-3.2291	0.2069	162	0.1836	3313	X-RAY DIFFRACTION	100
3.2291-3.5535	0.1974	172	0.1736	3299	X-RAY DIFFRACTION	100
3.5535-4.0665	0.1606	176	0.1633	3354	X-RAY DIFFRACTION	100
4.0665-5.1189	0.1512	138	0.1467	3384	X-RAY DIFFRACTION	100
5.1189-29.1164	0.1966	189	0.1899	3498	X-RAY DIFFRACTION	100

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