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- PDB-2pn5: Crystal Structure of TEP1r -

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Basic information

Entry
Database: PDB / ID: 2pn5
TitleCrystal Structure of TEP1r
ComponentsThioester-containing protein I
KeywordsIMMUNE SYSTEM / full-length mature peptide
Function / homology
Function and homology information


positive regulation of opsonization / positive regulation of phagocytosis, engulfment / endopeptidase inhibitor activity / immune system process / extracellular space
Similarity search - Function
Immunoglobulin-like - #2950 / : / TEP1, second CUB domain / 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 ...Immunoglobulin-like - #2950 / : / TEP1, second CUB domain / 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. / : / Alpha-macro-globulin thiol-ester bond-forming region / 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 allele S1
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.698 Å
AuthorsBaxter, R.H.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for conserved complement factor-like function in the antimalarial protein TEP1
Authors: Baxter, R.H.G. / Chang, C.I. / Chelliah, Y. / Blandin, S. / Levashina, E.A. / Deisenhofer, J.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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 / _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
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 I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6908
Polymers150,5331
Non-polymers1,1577
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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

#1: Protein Thioester-containing protein I / TEP1r


Mass: 150532.516 Da / Num. of mol.: 1 / Fragment: residues 22-1338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Description: Expression in BAC-TO-BAC system by INVITROGEN / Gene: TEP-I / Plasmid: pFastBac1 / Cell line (production host): High-Five(TM) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GYW4
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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 / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M NaH2/K2H PO4, 0.2 M NaCl, 0.1 M imidazole pH 8.0, 50 mM NaK tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: APS-1 / Detector: CCD / Date: Nov 11, 2006
Details: SAGITALLY FOCUSING. 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
8.414.82515210.1711.153.652979999.8
825.51800360.1431.1642251198.2
7.936.61789170.111.11422718100
5.847.21823320.131.273.63138898.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
9.885098.910.0391.3128
7.859.8899.610.0481.0678.7
6.867.8599.710.0941.1278.8
6.246.8699.910.1461.1638.9
5.796.2410010.1761.158.8
5.455.7910010.1821.2348.5
5.185.4510010.1781.1738.5
4.955.1810010.1771.1538.6
4.764.9510010.1831.1528.8
4.64.7699.910.2171.1548.8
4.454.610010.2351.1378.8
4.334.4510010.2851.1988.9
4.214.3310010.3251.1468.9
4.114.2110010.4021.1218.9
4.024.1110010.4711.0838.8
3.934.0210010.5931.1078.6
3.853.9310010.6591.1328.3
3.783.8599.910.7051.0877.9
3.713.7899.510.7371.17.1
3.653.7198.110.7091.1116.2
10.825095.520.0472.147.4
8.610.8296.920.0421.1678
7.528.697.520.0641.1028.1
6.847.5297.520.1021.0278.2
6.356.8498.120.1411.0618.2
5.976.3597.820.1741.1048.1
5.675.9797.920.1911.177.8
5.435.6798.520.1851.1547.6
5.225.4398.120.1851.0717.8
5.045.2298.520.1851.127.9
4.885.0498.620.1841.1088
4.744.8898.820.2031.1088
4.624.7498.320.2431.1348.1
4.54.6298.720.2371.1718.1
4.44.598.920.31.1098.1
4.314.498.920.3151.1078.1
4.224.3198.920.3621.0628.2
4.144.2298.920.4271.0618.1
4.074.1498.920.4761.1098.1
44.0798.920.5781.0938.1
10.825099.830.0362.0217.1
8.610.8210030.0341.297.7
7.528.610030.0511.1167.6
6.847.5210030.0771.0167.4
6.356.8410030.1061.0077.7
5.976.3510030.1351.0687.8
5.675.9710030.1521.1647.9
5.435.6710030.161.0647.9
5.225.4310030.1721.0777.9
5.045.2210030.1611.0458
4.885.0410030.1720.9948
4.744.8810030.1930.988
4.624.7410030.2250.9678
4.54.6210030.2350.9788.1
4.44.510030.2780.9958.1
4.314.410030.3060.948.1
4.224.3110030.3580.9928.1
4.144.2210030.4551.0558.1
4.074.1410030.5231.3038.1
44.0710030.6361.0368.1
9.755094.940.0432.0665.7
7.759.7597.240.0511.5585.8
6.777.7597.840.0821.385.8
6.156.779840.1081.3245.9
5.716.1598.340.1221.3616
5.385.7198.540.1161.3156
5.115.3898.940.1081.2686
4.895.1198.740.1081.3066
4.74.8998.840.1181.276
4.544.798.940.1221.266
4.394.5499.140.1431.1926
4.274.3999.140.1631.1936
4.164.2799.340.1841.1936
4.054.1699.240.221.1636
3.964.0599.440.2591.1136
3.883.9699.440.2981.115.9
3.83.8899.440.2921.0815.7
3.733.899.640.3260.9875.4
3.663.7399.740.3391.0175.1
3.63.6699.640.34514.8
ReflectionResolution: 2.698→50 Å / Num. all: 72031 / Num. obs: 71959 / % possible obs: 99.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 7.8 % / Biso Wilson estimate: 69.24 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.172 / Net I/σ(I): 10.1
Reflection shellResolution: 2.698→2.75 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3537 / Χ2: 1.033 / % possible all: 99.9

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Phasing

PhasingMethod: MIRAS
Phasing setD res high: 2.698 Å / D res low: 45.866 Å
Phasing dmFOM : 0.58 / FOM acentric: 0.57 / FOM centric: 0.61 / Reflection: 71858 / Reflection acentric: 64521 / Reflection centric: 7337
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-45.8660.940.940.9133462493853
4.8-7.70.870.870.84975883561402
3.9-4.80.830.840.7812071107721299
3.4-3.90.70.710.6212076109651111
2.9-3.40.420.430.3921409196911718
2.7-2.90.160.160.161319812244954
Phasing MIRResolution: 4→125.99 Å / FOM: 0.383 / FOM acentric: 0.36 / FOM centric: 0.518 / Reflection: 22771 / Reflection acentric: 19434 / Reflection centric: 3337
Phasing MIR der

Der set-ID: 1 / Resolution: 4→126 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
10.90.86122.61880.780.54193023071
20.910.89191.5301.80.670.44191943324
30.980.97253.6357.90.40.26193423086
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
26.18125.9910.910.88513.6661.50.330.273949
14.6126.1810.790.78251.3303.20.790.59274151
10.1314.6110.80.74178.2254.60.990.62723240
7.7510.1310.810.77141.6204.31.080.651409342
6.287.7510.810.8198.9147.21.30.852296421
5.286.2810.870.92104152.41.020.613433532
4.555.2810.950.93125.5168.90.650.464784618
44.5510.970.97120.71680.510.336344718
26.18125.9920.930.921364.115000.160.133850
14.6126.1820.850.82455.5532.80.530.43274169
10.1314.6120.860.86309.5418.60.70.45729265
7.7510.1320.850.83231.4327.80.840.521418375
6.287.7520.850.84165.5230.61.010.712311459
5.286.2820.890.91159.3225.90.870.563450579
4.555.2820.950.94190.3272.40.590.384782669
44.5520.960.95178.2244.50.490.326192758
26.18125.9930.990.981275.31392.80.10.093946
14.6126.1830.990.98329.9401.40.370.27273148
10.1314.6130.980.99330.9411.10.360.28720238
7.7510.1330.980.96331417.30.350.241408340
6.287.7530.970.94221.8309.80.490.322299420
5.286.2830.980.982222920.470.323436544
4.555.2830.980.97264.23580.370.244789626
44.5530.980.98238.7315.40.380.266378724
Phasing MIR der site
IDDer-IDBiso (Å)Atom type symbolFract xFract yFract zOccupancy
1179.732HG0.1660.7280.0110.687
2176.144HG0.0650.1880.0280.622
3192.05HG0.1920.1070.0720.606
4266.936HG0.1660.7290.0150.862
5277.731HG0.0650.1870.0260.928
6269.305HG0.1930.1060.0720.703
7281.421HG0.2890.4470.0450.53
8240.236HG0.4280.4680.120.238
9317.647XE0.1670.0550.1090.783
1036.899XE0.1150.6250.0210.479
Phasing MIR shell
Resolution (Å)FOMFOM acentricFOM centricReflectionReflection acentricReflection centric
26.18-125.990.5740.5460.596903951
14.61-26.180.5810.5780.584443274169
10.13-14.610.6080.6120.597994729265
7.75-10.130.5950.5910.61217931418375
6.28-7.750.5440.5220.65327742315459
5.28-6.280.4330.4120.55440363457579
4.55-5.280.3170.2970.4654784809669
4-4.550.2450.230.36871636393770

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RESOLVE2.09phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.698→45.88 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.901 / SU B: 22.325 / SU ML: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3631 5.1 %RANDOM
Rwork0.239 ---
all-71859 --
obs-71859 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: 52.085 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2--1.23 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 2.698→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10270 0 73 140 10483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210629
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.96914408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96251293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8524.688497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.161151885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.751555
X-RAY DIFFRACTIONr_chiral_restr0.0830.21630
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027968
X-RAY DIFFRACTIONr_nbd_refined0.2090.24386
X-RAY DIFFRACTIONr_nbtor_refined0.3090.27188
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2413
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.29
X-RAY DIFFRACTIONr_mcbond_it0.5031.56431
X-RAY DIFFRACTIONr_mcangle_it0.958210463
X-RAY DIFFRACTIONr_scbond_it1.21734304
X-RAY DIFFRACTIONr_scangle_it2.1594.53945
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 241 -
Rwork0.352 4919 -
obs-5160 100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.9999-1.042-1.48720.96130.13291.9637-0.02230.3909-0.358-0.11450.10410.08260.3056-0.2903-0.0818-0.0004-0.22170.04540.01250.0201-0.1467.08273.872143.35
20.4548-0.1233-0.28210.68810.00840.5730.1249-0.10890.00170.04230.0798-0.0895-0.0410.0788-0.2047-0.0642-0.0632-0.00310.0029-0.0282-0.1005102.64496.222135.654
32.5109-0.94290.08532.28760.76972.9166-0.1177-0.318-0.03050.36220.1599-0.08850.34160.203-0.04220.0760.03310.0065-0.0938-0.0197-0.1951114.71455.551111.635
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 2001 - 200
21400 - 660400 - 660
32201 - 399201 - 399
42661 - 771661 - 771
521164 - 13181164 - 1318
63772 - 1163772 - 1163

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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