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- PDB-3r0m: Crystal structure of anti-HIV llama VHH antibody A12 -

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Basic information

Entry
Database: PDB / ID: 3r0m
TitleCrystal structure of anti-HIV llama VHH antibody A12
ComponentsLlama VHH A12
KeywordsIMMUNE SYSTEM / Ig domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChen, L. / McLellan, J.S. / Kwon, Y.D. / Schmidt, S. / Wu, X. / Zhou, T. / Yang, Y. / Zhang, B. / Forsman, A. / Weiss, R.A. ...Chen, L. / McLellan, J.S. / Kwon, Y.D. / Schmidt, S. / Wu, X. / Zhou, T. / Yang, Y. / Zhang, B. / Forsman, A. / Weiss, R.A. / Verrips, T. / Mascola, J. / Kwong, P.D.
CitationJournal: To be Published
Title: Single-Headed Immunoglobulins Efficiently Penetrate CD4-Binding Site and Effectively Neutralize HIV-1
Authors: Chen, L. / McLellan, J.S. / Kwon, Y.D. / Schmidt, S. / Wu, X. / Zhou, T. / Yang, Y. / Zhang, B. / Forsman, A. / Weiss, R.A. / Verrips, T. / Mascola, J. / Kwong, P.D.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Llama VHH A12
B: Llama VHH A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3538
Polymers31,7772
Non-polymers5766
Water6,359353
1
A: Llama VHH A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1774
Polymers15,8881
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Llama VHH A12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1774
Polymers15,8881
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.884, 64.268, 81.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Llama VHH A12


Mass: 15888.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M imidazole pH 6.5, 1.4 M ammonium sulfate, 12% iso-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2010
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 49465 / Num. obs: 47240 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.2 / % possible all: 74.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→34.413 Å / SU ML: 0.15 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2166 2236 5.07 %RANDOM
Rwork0.1928 ---
all0.194 49420 --
obs0.194 44103 89.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.066 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.3352 Å2-0 Å2-0 Å2
2---7.2425 Å2-0 Å2
3----4.0927 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 30 353 2335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052026
X-RAY DIFFRACTIONf_angle_d0.9482746
X-RAY DIFFRACTIONf_dihedral_angle_d12.11710
X-RAY DIFFRACTIONf_chiral_restr0.066276
X-RAY DIFFRACTIONf_plane_restr0.003354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53230.3113930.28231728X-RAY DIFFRACTION60
1.5323-1.5680.27631280.24581969X-RAY DIFFRACTION68
1.568-1.60720.2731130.2352117X-RAY DIFFRACTION74
1.6072-1.65060.26611370.22082335X-RAY DIFFRACTION82
1.6506-1.69920.24071160.20922509X-RAY DIFFRACTION86
1.6992-1.7540.21771130.20132583X-RAY DIFFRACTION89
1.754-1.81670.19831360.19032654X-RAY DIFFRACTION92
1.8167-1.88950.20751510.18012740X-RAY DIFFRACTION93
1.8895-1.97540.18531460.18452672X-RAY DIFFRACTION93
1.9754-2.07960.20391420.18322868X-RAY DIFFRACTION97
2.0796-2.20990.22421390.18392890X-RAY DIFFRACTION98
2.2099-2.38040.19131650.19612850X-RAY DIFFRACTION98
2.3804-2.61990.23811640.20362919X-RAY DIFFRACTION99
2.6199-2.99880.25931870.20812901X-RAY DIFFRACTION99
2.9988-3.77750.21391500.18022991X-RAY DIFFRACTION100
3.7775-34.42190.18391560.17983141X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.6670.08070.21140.30480.03181.60580.067-0.00590.0160.0193-0.0592-0.0235-0.0914-0.0383-0.02240.09970.00630.01190.0909-0.00170.10851.0462-6.75712.3765
20.5228-0.05360.02490.60770.52791.70850.06440.03860.0066-0.1323-0.0422-0.04640.11670.0504-0.01970.1259-0.0016-0.00570.09140.00050.10521.1214-8.4814-12.3512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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