[English] 日本語
Yorodumi
- PDB-3nsw: Crystal Structure of Ancylostoma ceylanicum Excretory-Secretory P... -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / HEPES


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


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more