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- PDB-8gxv: Structure of a bacterial serpin Choloropin derived from Cholorobi... -

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Basic information

Entry
Database: PDB / ID: 8gxv
TitleStructure of a bacterial serpin Choloropin derived from Cholorobium limicola
ComponentsProteinase inhibitor I4 serpin
KeywordsDNA BINDING PROTEIN / Serpin / Serine Proteinase Inhibitor / Metastable conformation / DNA binding
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
Proteinase inhibitor I4 serpin
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, A. / Xu, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81870309 China
National Natural Science Foundation of China (NSFC)32070934 China
CitationJournal: To Be Published
Title: Climpin, a Novel Bacterial a Serpin inducing a Broad Range of Proteases and Regulated by Heparin and DNA.
Authors: Zhou, A. / Xu, J.
History
DepositionSep 21, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase inhibitor I4 serpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0386
Polymers41,6851
Non-polymers3545
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-122 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.660, 60.910, 130.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Proteinase inhibitor I4 serpin


Mass: 41684.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium limicola (strain DSM 245 / NBRC 103803 / 6330) (bacteria)
Gene: Clim_1363 / Production host: Escherichia coli (E. coli) / References: UniProt: B3ECZ8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG MME 550, 0.1M MES pH 6.5, 0.01M Zinc Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→60.91 Å / Num. obs: 25206 / % possible obs: 99.92 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02969 / Net I/σ(I): 15.11
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 2453 / CC1/2: 0.959 / CC star: 0.989

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
Cootmodel building
REFMAC5.8.0256refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EE5

6ee5


Resolution: 2.2→60.91 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1234 4.9 %
Rwork0.201 23960 -
obs0.2033 25194 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.57 Å2 / Biso mean: 30.4848 Å2 / Biso min: 14.97 Å2
Refinement stepCycle: final / Resolution: 2.2→60.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 10 59 2852
Biso mean--45.18 29.32 -
Num. residues----353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.290.28061220.208626052727
2.29-2.390.29121310.220126352766
2.39-2.520.32291300.221726382768
2.52-2.680.26491450.214425982743
2.68-2.880.28071640.220526292793
2.88-3.170.26761210.211726702791
3.17-3.630.22891500.194326492799
3.63-4.580.22141450.180926812826
4.58-60.910.21391260.194828552981
Refinement TLS params.Method: refined / Origin x: 2.7961 Å / Origin y: -20.5671 Å / Origin z: -21.0001 Å
111213212223313233
T0.1317 Å20.0164 Å20.0069 Å2-0.1729 Å2-0.0283 Å2--0.1362 Å2
L0.9714 °20.7537 °2-0.2834 °2-2.2018 °2-0.4933 °2--0.9484 °2
S0.1019 Å °-0.0391 Å °0.1051 Å °0.1097 Å °-0.0759 Å °0.1852 Å °-0.078 Å °-0.0112 Å °-0.0249 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 375
2X-RAY DIFFRACTION1allB2 - 64
3X-RAY DIFFRACTION1allC1 - 4
4X-RAY DIFFRACTION1allD1

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