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- PDB-3mac: crystal structure of GP41-derived protein complexed with fab 8062 -

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Basic information

Entry
Database: PDB / ID: 3mac
Titlecrystal structure of GP41-derived protein complexed with fab 8062
Components
  • (Fab8062) x 2
  • Transmembrane glycoprotein
KeywordsIMMUNE SYSTEM / GP41 / fab8062
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #1860 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Transmembrane glycoprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, M. / Gustchina, E. / Louis, J. / Gustchina, A. / Wlodawer, A. / Clore, M.
CitationJournal: Plos Pathog. / Year: 2010
Title: Structural Basis of HIV-1 Neutralization by Affinity Matured Fabs Directed against the Internal Trimeric Coiled-Coil of gp41.
Authors: Gustchina, E. / Li, M. / Louis, J.M. / Anderson, D.E. / Lloyd, J. / Frisch, C. / Bewley, C.A. / Gustchina, A. / Wlodawer, A. / Clore, G.M.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: 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 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane glycoprotein
H: Fab8062
L: Fab8062


Theoretical massNumber of molelcules
Total (without water)73,4553
Polymers73,4553
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-39 kcal/mol
Surface area28920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.668, 41.741, 98.602
Angle α, β, γ (deg.)90.00, 94.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transmembrane glycoprotein


Mass: 24479.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWW0
#2: Antibody Fab8062


Mass: 26334.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#3: Antibody Fab8062


Mass: 22640.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% Polyethylene glycol 10K, 0.1M ammonium sulfate, 5% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARCCD300 / Detector: CCD / Date: Jan 1, 2009 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→29.5 Å / Num. obs: 23655 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rsym value: 0.082 / Net I/σ(I): 13.79
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.524 / % possible all: 96.7

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0104refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CMR

2cmr


Resolution: 2.5→29.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 21.692 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.602 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26441 728 3.1 %RANDOM
Rwork0.19961 ---
obs0.20163 22917 98.59 %-
all-23655 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.229 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å2-1.58 Å2
2---0.25 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4798 0 0 69 4867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224900
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9456669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24325.628215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2815808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3361516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213697
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.40523085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3934977
X-RAY DIFFRACTIONr_scbond_it1.80121815
X-RAY DIFFRACTIONr_scangle_it2.64931691
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 46 -
Rwork0.229 1525 -
obs--88.86 %
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)
14.2947-0.40640.52163.86390.86045.416-0.0278-0.07130.3297-0.19370.12380.2948-0.9098-0.3249-0.0960.25160.039-0.0260.1249-0.01340.12459.681236.261434.4561
24.0079-1.02931.26022.3309-1.01446.21570.15850.04710.20190.0078-0.2314-0.0666-0.35550.06110.07290.14480.01710.01240.05-0.01730.065818.912436.54570.8141
31.3435-0.80051.15260.61470.05875.1749-0.0801-0.0021-0.04180.02660.12020.038-0.0720.6667-0.04010.1098-0.0331-0.01130.2976-0.01010.088225.547921.486434.1875
40.13180.2055-0.25510.5389-0.03414.92810.00540.0525-0.02860.1463-0.0267-0.00790.35670.22860.02130.21220.04660.02430.1776-0.01850.132919.49220.331768.2636
53.51170.43450.99151.31950.11182.2161-0.06240.0280.0657-0.03020.0084-0.0044-0.04130.27720.0540.19780.01890.020.04060.00140.16711.795323.41875.4005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 104
2X-RAY DIFFRACTION2L105 - 211
3X-RAY DIFFRACTION3H1 - 106
4X-RAY DIFFRACTION4H107 - 224
5X-RAY DIFFRACTION5A1 - 217

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