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- PDB-4c1a: Coiled coil domain of the ZfL2-1 ORF1 protein from the zebrafish ... -

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Basic information

Entry
Database: PDB / ID: 4c1a
TitleCoiled coil domain of the ZfL2-1 ORF1 protein from the zebrafish ZfL2- 1 retrotransposon
ComponentsORF1-ENCODED PROTEIN
KeywordsHYDROLASE / RETROTRANSPOSITION / RNA-BINDING / MEMBRANE-BINDING / LIPID-BINDING / SELF-ASSOCIATION
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / ORF1-encoded protein
Function and homology information
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchneider, A.M. / Weichenrieder, O.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structure and Properties of the Esterase from Non-Ltr Retrotransposons Suggest a Role for Lipids in Retrotransposition.
Authors: Schneider, A.M. / Schmidt, S. / Jonas, S. / Vollmer, B. / Khazina, E. / Weichenrieder, O.
History
DepositionAug 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF1-ENCODED PROTEIN
B: ORF1-ENCODED PROTEIN
C: ORF1-ENCODED PROTEIN
D: ORF1-ENCODED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0049
Polymers16,5434
Non-polymers4605
Water2,090116
1
A: ORF1-ENCODED PROTEIN
B: ORF1-ENCODED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3643
Polymers8,2722
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-22.4 kcal/mol
Surface area5630 Å2
MethodPISA
2
C: ORF1-ENCODED PROTEIN
D: ORF1-ENCODED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6406
Polymers8,2722
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-20.4 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.730, 52.420, 51.830
Angle α, β, γ (deg.)90.00, 99.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
ORF1-ENCODED PROTEIN / ZFL2-1 ORF1P


Mass: 4135.833 Da / Num. of mol.: 4 / Fragment: COILED COIL DOMAIN, RESIDUES 15-47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Description: SYNTHETIC CODON-OPTIMIZED DNA SEQUENCE / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q3LG57
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE THREE N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. THE SAMPLE WAS PROTEOLYZED PRIOR TO ...THE THREE N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. THE SAMPLE WAS PROTEOLYZED PRIOR TO CRYSTALLIZATION.

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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: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7.5 / Details: 200MM NA-THIOCYANATE, 20% PEG 3350, PH=7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97138
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97138 Å / Relative weight: 1
ReflectionResolution: 1.55→37 Å / Num. obs: 17462 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.06 / Net I/σ(I): 10.3
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.47 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A92

1a92


Resolution: 1.55→36.583 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 26.14 / Stereochemistry target values: ML / Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.2145 905 5.2 %
Rwork0.1862 --
obs0.1877 17443 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 1.55→36.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 30 116 1259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131138
X-RAY DIFFRACTIONf_angle_d1.3931514
X-RAY DIFFRACTIONf_dihedral_angle_d15.569471
X-RAY DIFFRACTIONf_chiral_restr0.062182
X-RAY DIFFRACTIONf_plane_restr0.006194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5502-1.64730.33891560.27362671X-RAY DIFFRACTION93
1.6473-1.77450.25371390.21582766X-RAY DIFFRACTION96
1.7745-1.9530.28831490.2052812X-RAY DIFFRACTION97
1.953-2.23560.19711560.16272756X-RAY DIFFRACTION96
2.2356-2.81650.18951370.17212768X-RAY DIFFRACTION95
2.8165-36.59280.19531680.18152765X-RAY DIFFRACTION95
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)
10.3090.51890.01530.62020.04130.1246-0.0665-0.0555-0.13230.027-0.0571-0.053-0.17480.1483-0.01070.1350.0275-0.00030.14210.02340.097915.195226.212839.4591
20.3461-0.2871-0.05320.3685-0.05730.0576-0.1269-0.0054-0.12640.0527-0.05020.1316-0.2492-0.0669-0.02240.15730.00060.00430.10170.00070.12297.039726.384637.6957
30.27590.2538-0.23520.622-0.43360.2794-0.0602-0.11430.14350.0092-0.03230.07630.0114-0.08480.02730.0821-0.00580.0070.1134-0.02790.1195-4.296640.968939.6061
40.51870.1099-0.3640.2520.10830.3139-0.11530.16030.0747-0.06-0.0532-0.19660.0160.2764-0.00150.0782-0.00670.00690.11250.01420.15912.936241.15535.6717
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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