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- PDB-4d94: Crystal Structure of TEP1r -

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Basic information

Entry
Database: PDB / ID: 4d94
TitleCrystal Structure of TEP1r
ComponentsThioester-containing protein 1
KeywordsIMMUNE SYSTEM / Plasmodium refractory allele / full-length protein / thioester / macroglobulin domains / component of innate immune response by the opsinization and melanization of pathogens
Function / homology
Function and homology information


endopeptidase inhibitor activity / extracellular space
Similarity search - Function
Jelly Rolls - #1540 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / Alpha-2-macroglobulin, TED domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Glycosyltransferase - #20 ...Jelly Rolls - #1540 / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / S-adenosyl-L-methionine-dependent methyltransferases / Alpha-2-macroglobulin, TED domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Glycosyltransferase - #20 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Single Sheet / Jelly Rolls / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Thioester-containing protein 1
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.7 Å
AuthorsLe, B.V. / Williams, M. / Logarajah, S. / Baxter, R.H.G.
CitationJournal: Plos Pathog. / Year: 2012
Title: Molecular Basis for Genetic Resistance of Anopheles gambiae to Plasmodium: Structural Analysis of TEP1 Susceptible and Resistant Alleles.
Authors: Le, B.V. / Williams, M. / Logarajah, S. / Baxter, R.H.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioester-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,9679
Polymers150,5771
Non-polymers1,3918
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Thioester-containing protein 1
hetero molecules

A: Thioester-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,93418
Polymers301,1532
Non-polymers2,78116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7360 Å2
ΔGint-36 kcal/mol
Surface area116200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.515, 150.515, 226.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thioester-containing protein 1


Mass: 150576.516 Da / Num. of mol.: 1 / Fragment: residues 22-1338
Source method: isolated from a genetically manipulated source
Details: Expression in Bac to Bac System by Invitrogen
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Strain: L3-5 / Gene: tep1 / Plasmid: pFastBacI / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C9XI66

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Sugars , 2 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 136 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 4.26 Å3/Da / Density % sol: 71.1 %
Crystal growTemperature: 294 K / pH: 6.5
Details: 2 M NaH2/K2H PO4, 0.2 M NaCl, 0.1 M imidazole pH 8.0, 50 mM NaK tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.92
DetectorType: SBC-3 / Detector: CCD / Date: Nov 11, 2006 / Details: SI (111)
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→45.88 Å / Num. obs: 71959 / % possible obs: 99.9 % / Observed criterion σ(I): -1 / Redundancy: 7.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.898 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
MLPHAREphasing
REFMAC5.1refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MIRAS / Resolution: 2.7→45.866 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU ML: 0.37 / σ(F): 1.33 / Phase error: 25.16 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rfree0.2442 3631 5.05 %
Rwork0.2193 --
obs0.2206 71850 99.76 %
all-68403 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.17 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7934 Å20 Å2-0 Å2
2--1.7934 Å2-0 Å2
3----3.5868 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10207 0 87 133 10427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510564
X-RAY DIFFRACTIONf_angle_d1.01814313
X-RAY DIFFRACTIONf_dihedral_angle_d16.0543957
X-RAY DIFFRACTIONf_chiral_restr0.0581627
X-RAY DIFFRACTIONf_plane_restr0.0041828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6981-2.73360.43141250.37692550X-RAY DIFFRACTION98
2.7336-2.7710.37121280.34772601X-RAY DIFFRACTION100
2.771-2.81060.37791470.31962547X-RAY DIFFRACTION100
2.8106-2.85260.33381500.30322596X-RAY DIFFRACTION100
2.8526-2.89710.30961280.27732619X-RAY DIFFRACTION100
2.8971-2.94460.30691290.28142582X-RAY DIFFRACTION100
2.9446-2.99540.33071190.27392609X-RAY DIFFRACTION100
2.9954-3.04980.30781490.27182596X-RAY DIFFRACTION100
3.0498-3.10850.29451190.26742592X-RAY DIFFRACTION100
3.1085-3.17190.27071440.26912608X-RAY DIFFRACTION100
3.1719-3.24090.28441470.25512600X-RAY DIFFRACTION100
3.2409-3.31620.28031250.26522610X-RAY DIFFRACTION100
3.3162-3.39910.28941550.25042591X-RAY DIFFRACTION100
3.3991-3.4910.25991270.24442625X-RAY DIFFRACTION100
3.491-3.59370.23961410.23122588X-RAY DIFFRACTION100
3.5937-3.70960.28141720.21692576X-RAY DIFFRACTION100
3.7096-3.84220.22511480.21772612X-RAY DIFFRACTION100
3.8422-3.99590.21991380.20562610X-RAY DIFFRACTION100
3.9959-4.17770.24071530.18632629X-RAY DIFFRACTION100
4.1777-4.39780.18471390.17372606X-RAY DIFFRACTION100
4.3978-4.6730.17261220.14582674X-RAY DIFFRACTION100
4.673-5.03340.15751430.15532656X-RAY DIFFRACTION100
5.0334-5.53920.2271210.17822692X-RAY DIFFRACTION100
5.5392-6.33890.21431520.22012687X-RAY DIFFRACTION100
6.3389-7.97960.2781460.20812720X-RAY DIFFRACTION100
7.9796-45.87220.21751640.22172843X-RAY DIFFRACTION99
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)
12.0803-0.4551-0.98360.8097-0.00591.2506-0.01810.3711-0.2674-0.10010.06360.10950.1447-0.3295-0.04950.4788-0.16240.03630.56380.01890.395467.501373.9575143.2112
20.2503-0.1462-0.27641.48641.00241.33470.0452-0.11940.03720.13150.0387-0.15940.17170.1571-0.03030.08230.0033-0.02670.172-0.04570.1362113.27374.433120.065
33.66330.92350.5832.13970.28172.52060.11290.32360.51440.0540.28770.669-0.0944-0.1674-0.36230.490.0070.20790.48170.24170.622166.0045104.66161.7267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:221 OR RESID 422:685 ) )A22 - 221
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 22:221 OR RESID 422:685 ) )A422 - 685
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 222:326 OR RESID 686:1338 ) )A222 - 326
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 222:326 OR RESID 686:1338 ) )A686 - 1338
5X-RAY DIFFRACTION3( CHAIN A AND RESID 327:421 )A327 - 421

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