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- PDB-2q8b: Structure of the malaria antigen AMA1 in complex with a growth-in... -

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Basic information

Entry
Database: PDB / ID: 2q8b
TitleStructure of the malaria antigen AMA1 in complex with a growth-inhibitory antibody
Components
  • 1F9 heavy chain
  • 1F9 light chain
  • Apical membrane antigen 1
KeywordsIMMUNE SYSTEM / antigen-antibody complex
Function / homology
Function and homology information


apical complex / microneme / host cell surface binding / symbiont entry into host / membrane
Similarity search - Function
Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Immunoglobulins / Immunoglobulin-like / Sandwich ...Apical membrane antigen 1 domain superfamily / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Apical membrane antigen 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGupta, A. / Murphy, V.J. / Anders, R.F. / Batchelor, A.H.
CitationJournal: Plos Pathog. / Year: 2007
Title: Structure of the Malaria Antigen AMA1 in Complex with a Growth-Inhibitory Antibody
Authors: Coley, A.M. / Gupta, A. / Murphy, V.J. / Bai, T. / Kim, H. / Foley, M. / Anders, R.F. / Batchelor, A.H.
History
DepositionJun 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apical membrane antigen 1
L: 1F9 light chain
H: 1F9 heavy chain


Theoretical massNumber of molelcules
Total (without water)84,4893
Polymers84,4893
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.905, 51.487, 95.257
Angle α, β, γ (deg.)90.00, 108.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

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Components

#1: Protein Apical membrane antigen 1


Mass: 38417.102 Da / Num. of mol.: 1 / Fragment: Domains I and II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: AMA1 / Plasmid: pPROEXHTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7KQK5
#2: Antibody 1F9 light chain


Mass: 23698.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma cell line / Source: (natural) Mus musculus (house mouse)
#3: Antibody 1F9 heavy chain


Mass: 22373.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma cell line / Source: (natural) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM MES, 10 mM MnCl2, 6 % PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 7, 2004 / Details: Osmic multilayer mirrors
RadiationMonochromator: Osmic multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 36116 / Num. obs: 36116 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.057 / Net I/σ(I): 14
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4 / Rsym value: 0.29 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z40, 2CGR

1z40

2cgr


Resolution: 2.3→27.95 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 13.046 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25565 1899 5 %RANDOM
Rwork0.20914 ---
all0.21152 36116 --
obs0.21152 36116 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.36 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å20 Å2-0.68 Å2
2--1.29 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5378 0 0 220 5598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9437539
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3725.126238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47615829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4651514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024247
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1760.22235
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23664
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2329
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3581.53600
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63625672
X-RAY DIFFRACTIONr_scbond_it0.91532228
X-RAY DIFFRACTIONr_scangle_it1.4814.51867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 135 -
Rwork0.255 2594 -
obs--100 %
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)
13.8147-0.00990.9970.89490.00021.49190.03450.0801-0.2311-0.068-0.03560.02780.0536-0.20130.0011-0.19850.00410.0381-0.3216-0.011-0.191913.6529-11.255240.1561
27.4672-0.4431.7952.7463-1.22316.2943-0.39791.15880.602-0.16510.1074-0.281-0.4991-0.1930.2905-0.0214-0.0159-0.03770.17510.1142-0.1113-10.79836.602113.0479
310.7284.32033.5184.05180.66087.84020.04570.31740.1513-0.71780.13660.80380.1885-0.1428-0.18230.3906-0.0021-0.19910.6036-0.18030.1742-36.6413-8.2443-10.2787
46.6203-0.33081.4472.4886-1.61214.1916-0.2703-0.3738-0.06410.1930.42170.2591-0.3648-1.1197-0.1514-0.10860.18220.04090.32010.0677-0.1845-24.5483-1.538228.5288
58.63250.3447-0.94716.13867.102222.28250.1903-0.5626-1.10250.05470.02760.1471.9239-0.1888-0.21790.2933-0.0716-0.18720.5050.08480.349-35.5331-18.39232.6248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA105 - 4383 - 336
2X-RAY DIFFRACTION2LB1 - 1061 - 106
3X-RAY DIFFRACTION3LB107 - 213107 - 213
4X-RAY DIFFRACTION4HC1 - 1101 - 110
5X-RAY DIFFRACTION5HC111 - 210111 - 210

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