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- PDB-3nsw: Crystal Structure of Ancylostoma ceylanicum Excretory-Secretory P... -

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Basic information

Entry
Database: PDB / ID: 3nsw
TitleCrystal Structure of Ancylostoma ceylanicum Excretory-Secretory Protein 2
ComponentsExcretory-secretory protein 2
KeywordsIMMUNE SYSTEM / Ancylostoma ceylanicum / hookworm / excretory-secretory protein / merohedral twinning / immunomodulator / netrin domain
Function / homologyOB fold (Dihydrolipoamide Acetyltransferase, E2P) - #780 / : / Excretory-secretory protein 2 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Excretory-secretory protein 2
Function and homology information
Biological speciesAncylostoma ceylanicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKucera, K. / Modis, Y.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Ancylostoma ceylanicum Excretory-Secretory Protein 2 Adopts a Netrin-Like Fold and Defines a Novel Family of Nematode Proteins.
Authors: Kucera, K. / Harrison, L.M. / Cappello, M. / Modis, Y.
History
DepositionJul 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Nov 20, 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: Excretory-secretory protein 2
B: Excretory-secretory protein 2
C: Excretory-secretory protein 2
D: Excretory-secretory protein 2
E: Excretory-secretory protein 2
F: Excretory-secretory protein 2
G: Excretory-secretory protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9419
Polymers84,5857
Non-polymers3562
Water16,718928
1
A: Excretory-secretory protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2022
Polymers12,0841
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Excretory-secretory protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3222
Polymers12,0841
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Excretory-secretory protein 2


Theoretical massNumber of molelcules
Total (without water)12,0841
Polymers12,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Excretory-secretory protein 2


Theoretical massNumber of molelcules
Total (without water)12,0841
Polymers12,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Excretory-secretory protein 2


Theoretical massNumber of molelcules
Total (without water)12,0841
Polymers12,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Excretory-secretory protein 2


Theoretical massNumber of molelcules
Total (without water)12,0841
Polymers12,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Excretory-secretory protein 2


Theoretical massNumber of molelcules
Total (without water)12,0841
Polymers12,0841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.212, 52.212, 345.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Excretory-secretory protein 2


Mass: 12083.514 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: Expressed with an N-terminal 6x histidine tag and thrombin cleavage sequence. Thrombin cleavage prior to crystallization left non-native Gly-Ser-His in the crystallization construct.
Source: (gene. exp.) Ancylostoma ceylanicum (invertebrata) / Gene: ES-2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2(DE3) / References: UniProt: Q6R7N7
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid (HEPES), 60% (4S)-2-Methyl-2,4-pentanediol (MPD), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 28, 2009
Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification.
RadiationMonochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.768
11-H, K, -L20.232
ReflectionResolution: 1.75→36.91 Å / Num. obs: 79362 / % possible obs: 90.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.498
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.326 / Num. unique all: 3110 / % possible all: 52.3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STARTING MODEL: THE STRUCTURE OF ACEES-2 WAS SOLVED USING A LEAD (PBNO3) SOAKED CRYSTAL AND SAD METHODS AT 2.0 ANGSTROM RESOLUTION

Resolution: 1.75→36.91 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.981 / SU ML: 0.042 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Used amplitude-based twin refinement with twin operator: H, K, L fraction = 0.759 and -H, K, -L fraction = 0.241.
RfactorNum. reflection% reflectionSelection details
Rfree0.17466 4180 5 %RANDOM
Rwork0.1463 ---
obs0.14773 79362 90.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.251 Å2
Baniso -1Baniso -2Baniso -3
1-7.05 Å20 Å2-0 Å2
2--7.05 Å20 Å2
3----14.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.02 Å0.021 Å
Luzzati sigma a-0.042 Å
Refinement stepCycle: LAST / Resolution: 1.75→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5815 0 23 928 6766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226177
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.9648410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63325.185297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.779151101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4611529
X-RAY DIFFRACTIONr_chiral_restr0.070.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214669
X-RAY DIFFRACTIONr_mcbond_it3.392103727
X-RAY DIFFRACTIONr_mcangle_it5.2206052
X-RAY DIFFRACTIONr_scbond_it6.973252450
X-RAY DIFFRACTIONr_scangle_it8.853302333
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 159 -
Rwork0.319 3110 -
obs-3110 47.54 %
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)
12.1244-1.10810.87253.102-0.9313.0204-0.11170.0566-0.00770.17060.11640.0845-0.1358-0.0452-0.00470.06450.04590.01690.04340.01590.0964-3.41711.322-13.457
21.6125-0.3479-0.68342.62520.84722.6876-0.0328-0.0036-0.0449-0.03040.02930.1126-0.0622-0.13750.00350.05180.03990.0170.03760.02680.123214.215-9.336-24.628
31.4411-0.57920.22432.1998-0.58923.1108-0.01920.13460.0926-0.164-0.1351-0.02030.06340.08070.15420.10830.02850.00230.0631-0.00020.064811.63822.03719.444
41.6735-0.4553-0.32852.21270.04463.2484-0.1107-0.2166-0.06180.11740.07970.0013-0.1165-0.10960.0310.08640.0640.03610.06160.0330.096628.08724.374-4.864
51.79160.42081.20193.23811.21563.41640.0738-0.1278-0.08780.0415-0.07320.08890.1517-0.1894-0.00060.12740.0133-0.01240.0240.02860.1203-6.343-8.7238.802
61.38190.2694-0.10221.964-0.17562.0879-0.10060.0226-0.03290.06540.02750.07330.07520.07260.07310.04670.02350.02720.04360.00890.082931.49111.114-36.53
75.35980.39472.32281.6269-0.84311.9573-0.13280.8196-0.1001-0.180.1029-0.11160.10220.00880.02990.2286-0.0560.02670.462-0.06570.31138.286-27.886-50.283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 102
2X-RAY DIFFRACTION2B-3 - 102
3X-RAY DIFFRACTION3C-3 - 102
4X-RAY DIFFRACTION4D-3 - 102
5X-RAY DIFFRACTION5E-3 - 102
6X-RAY DIFFRACTION6F-3 - 102
7X-RAY DIFFRACTION7G-3 - 102

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