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- PDB-7zjo: Phosphorylated Thalassospira sp. esterase -

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Basic information

Entry
Database: PDB / ID: 7zjo
TitlePhosphorylated Thalassospira sp. esterase
ComponentsLipase
KeywordsHYDROLASE / esterase / lipase / inhibitor / complex / phosphorylated
Function / homologyP-NITROPHENOL / :
Function and homology information
Biological speciesThalassospira sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLund, B.A.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway262695 Norway
Research Council of Norway274858 Norway
CitationJournal: To Be Published
Title: Phosphorylated Thalassospira sp. esterase
Authors: Lund, B.A.
History
DepositionApr 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase
B: Lipase
C: Lipase
D: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,50921
Polymers136,7684
Non-polymers1,74117
Water14,124784
1
C: Lipase
hetero molecules

A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,16810
Polymers68,3842
Non-polymers7848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
2
B: Lipase
D: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,34111
Polymers68,3842
Non-polymers9579
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.210, 115.768, 87.554
Angle α, β, γ (deg.)90.000, 90.059, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Lipase


Mass: 34191.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thalassospira sp. (bacteria) / Gene: CMO05_03125 / Plasmid: pET-26b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Nico21(DE3) / References: UniProt: A0A2E9W914

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Non-polymers , 5 types, 801 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.99 Å3/Da / Density % sol: 58.82 % / Description: plate-like
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0 M Ammonium sulfate, 0.1 M Sodium HEPES 7.5, 2 % v/v PEG 400 (Structure HT C6)
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.95→64.1 Å / Num. obs: 113113 / % possible obs: 96.78 % / Redundancy: 1.7 % / Biso Wilson estimate: 27.25 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.07344 / Net I/σ(I): 7.91
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.3682 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 11168 / CC1/2: 0.797

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
pointless1.11.21data scaling
PHASER2.8.3phasing
XDSdata reduction
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V2I

4v2i


Resolution: 1.95→64.1 Å / SU ML: 0.1865 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 20.5338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 1658 1.47 %
Rwork0.1672 111445 -
obs0.1676 113103 96.79 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.87 Å2
Refinement stepCycle: LAST / Resolution: 1.95→64.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9566 0 113 784 10463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00939958
X-RAY DIFFRACTIONf_angle_d0.920713613
X-RAY DIFFRACTIONf_chiral_restr0.05591546
X-RAY DIFFRACTIONf_plane_restr0.00961795
X-RAY DIFFRACTIONf_dihedral_angle_d8.65081428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.26451360.24459194X-RAY DIFFRACTION96.38
2.01-2.070.25961360.21799184X-RAY DIFFRACTION95.99
2.07-2.150.2521400.20219161X-RAY DIFFRACTION95.93
2.15-2.230.22271400.18419202X-RAY DIFFRACTION96.4
2.23-2.330.23961380.1719305X-RAY DIFFRACTION96.86
2.33-2.460.2091400.16199267X-RAY DIFFRACTION97.17
2.46-2.610.21811310.15539291X-RAY DIFFRACTION96.77
2.61-2.810.18491370.15359333X-RAY DIFFRACTION97.05
2.81-3.10.19191430.15329349X-RAY DIFFRACTION97.46
3.1-3.540.2071410.169315X-RAY DIFFRACTION97.09
3.54-4.460.15961380.14999361X-RAY DIFFRACTION97.13
4.46-64.10.18231380.17479483X-RAY DIFFRACTION97.21
Refinement TLS params.Method: refined / Origin x: 54.2926272693 Å / Origin y: 0.648329264225 Å / Origin z: 64.4391974898 Å
111213212223313233
T0.183580045839 Å2-0.00879785407355 Å20.0107327047214 Å2-0.202758425385 Å2-0.00551766386643 Å2--0.190367714203 Å2
L0.148798568674 °20.0684298191943 °20.0559805835696 °2-0.206285621418 °20.0305405291553 °2--0.175648412674 °2
S-0.0191871070666 Å °-0.0413778723272 Å °-0.0225732360708 Å °-0.0207706917048 Å °-0.0089725527981 Å °0.0192192781491 Å °0.0290065838378 Å °-0.0490920443423 Å °0.031698854408 Å °
Refinement TLS groupSelection details: all

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