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- PDB-4c1b: Esterase domain of the ZfL2-1 ORF1 protein from the zebrafish ZfL... -

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Basic information

Entry
Database: PDB / ID: 4c1b
TitleEsterase 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 / homologyRossmann fold - #12690 / Rossmann fold - #12700 / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ORF1-encoded protein
Function and homology information
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.501 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 1.2Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_source
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)57,4233
Polymers57,4233
Non-polymers00
Water1,33374
1
A: ORF1-ENCODED PROTEIN
B: ORF1-ENCODED PROTEIN


Theoretical massNumber of molelcules
Total (without water)38,2822
Polymers38,2822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-39.3 kcal/mol
Surface area17190 Å2
MethodPISA
2
C: ORF1-ENCODED PROTEIN

C: ORF1-ENCODED PROTEIN


Theoretical massNumber of molelcules
Total (without water)38,2822
Polymers38,2822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area5530 Å2
ΔGint-39.3 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.260, 111.260, 115.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 19141.092 Da / Num. of mol.: 3 / Fragment: SGNH ESTERASE DOMAIN, RESIDUES 136-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Description: SYNTHETIC CODON-OPTIMIZED DNA SEQUENCE / Plasmid: PETM41P / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: Q3LG57, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FOUR N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG.

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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: 3.2 Å3/Da / Density % sol: 62 %
Description: GOLD SITES WERE IDENTIFIED BY SIRAS, USING THE SECOND DATASET, COLLECTED AT 1.0397 A, PEAK DATA AT THE AU LIII-EDGE.
Crystal growpH: 7
Details: 100 MM NA-HEPES PH=7.0, 0.5% JEFFAMINE, 1.1M NA-MALONATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0, 1.0397
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2011 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.03971
ReflectionResolution: 2.5→46 Å / Num. obs: 24355 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 51.51 Å2 / Rsym value: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.501→45.709 Å / SU ML: 0.3 / σ(F): 2.04 / Phase error: 21.04 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN B, RESIDUES 132 TO 134. CHAIN C, RESIDUES 132 TO 134, 151 TO 155, 180 TO 183 AND 302.
RfactorNum. reflection% reflection
Rfree0.2099 1244 5.1 %
Rwork0.1672 --
obs0.1694 24346 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.6 Å2
Refinement stepCycle: LAST / Resolution: 2.501→45.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3951 0 0 74 4025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114031
X-RAY DIFFRACTIONf_angle_d1.1825460
X-RAY DIFFRACTIONf_dihedral_angle_d14.141519
X-RAY DIFFRACTIONf_chiral_restr0.06623
X-RAY DIFFRACTIONf_plane_restr0.006699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5007-2.60080.28071370.2192533X-RAY DIFFRACTION100
2.6008-2.71910.22251370.19672583X-RAY DIFFRACTION100
2.7191-2.86250.23241550.18032536X-RAY DIFFRACTION100
2.8625-3.04180.21631190.18692558X-RAY DIFFRACTION100
3.0418-3.27660.24121290.19082578X-RAY DIFFRACTION100
3.2766-3.60620.22771570.17772552X-RAY DIFFRACTION100
3.6062-4.12770.23251320.15882574X-RAY DIFFRACTION100
4.1277-5.19930.16861410.14412570X-RAY DIFFRACTION100
5.1993-45.7170.1921370.1572618X-RAY DIFFRACTION100
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)
12.87460.3272-0.75611.53030.22280.9753-0.1378-0.34140.44660.21460.09560.2639-0.2912-0.3924-0.00010.39340.059-0.00320.3982-0.03590.36118.488472.1829-7.961
23.92790.3218-0.68023.77391.23772.1259-0.2513-0.1746-0.39520.30220.08450.15960.140.0519-0.00610.36920.02570.05980.26010.05970.338845.254544.32199.4634
33.92020.24480.46092.87522.52182.3146-0.1593-0.3464-0.7030.37480.05510.63640.6415-0.6022-0.00790.4295-0.02790.12270.42070.04330.652234.800138.03239.9574
43.4460.73091.72841.0545-0.57042.9909-0.22760.01710.4924-0.05930.0870.0976-0.47850.0008-0.00710.36580.0391-0.08890.2897-0.0320.306131.690877.3539-12.7442
51.6841-0.65040.99651.2880.59641.54680.02180.91740.5047-0.7263-0.13090.28760.09610.1345-0.00470.69670.05080.03030.94450.23710.490257.309374.8599-32.7893
62.4839-0.32560.02632.25220.35222.82340.06260.488-0.5976-0.5274-0.12220.6241-0.1767-0.3872-0.01390.43-0.0035-0.06960.5898-0.18860.550150.420136.8792-21.6479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 132 THROUGH 200 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 201 THROUGH 302 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 135 THROUGH 200 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 238 THROUGH 302 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 135 THROUGH 200 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 201 THROUGH 301 )

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