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- PDB-6f4u: Crystal structure of reactive loop cleaved kallistatin at 1.9 ang... -

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Basic information

Entry
Database: PDB / ID: 6f4u
TitleCrystal structure of reactive loop cleaved kallistatin at 1.9 angstrom resolution
Components(Kallistatin) x 2
KeywordsHYDROLASE / inhibitor / Serpin / kallekrein / kallistatin
Function / homology
Function and homology information


platelet dense granule lumen / Developmental Lineage of Pancreatic Acinar Cells / serine-type endopeptidase inhibitor activity / Platelet degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsZhou, A. / Wei, Z. / Lin, F.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
British Heart Foundation United Kingdom
NSFC81572090 China
CitationJournal: To Be Published
Title: Crystal structure of human Kallistatin
Authors: Zhou, A. / Ma, L.
History
DepositionNov 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallistatin
D: Kallistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,27713
Polymers43,6002
Non-polymers67711
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-39 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.510, 113.510, 76.172
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#1: Protein Kallistatin / Kallikrein inhibitor / Peptidase inhibitor 4 / PI-4 / Serpin A4


Mass: 39031.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: reactive loop cleaved human kallistatin with an Extra Gly at the N-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA4, KST, PI4 / Plasmid: Psumo3-Kal / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29622
#2: Protein/peptide Kallistatin / Kallikrein inhibitor / Peptidase inhibitor 4 / PI-4 / Serpin A4


Mass: 4568.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: reactive loop cleaved human kallistatin with an Extra Gly at the N-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA4, KST, PI4 / Plasmid: Psumo3-Kal / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29622

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Non-polymers , 5 types, 201 molecules

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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 3.25 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% tertbutanal

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.196 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jan 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.196 Å / Relative weight: 1
ReflectionResolution: 1.9→35.67 Å / Num. obs: 44414 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 14
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6433 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.9→98.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.288 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19526 2208 5 %RANDOM
Rwork0.16706 ---
obs0.16848 41647 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.9→98.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 42 190 3246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193178
X-RAY DIFFRACTIONr_bond_other_d0.0020.023012
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9644296
X-RAY DIFFRACTIONr_angle_other_deg0.89936982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61523.404141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0515557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7631517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02678
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2392.4361512
X-RAY DIFFRACTIONr_mcbond_other1.2372.4341511
X-RAY DIFFRACTIONr_mcangle_it2.0013.6371893
X-RAY DIFFRACTIONr_mcangle_other23.6391894
X-RAY DIFFRACTIONr_scbond_it1.4692.731666
X-RAY DIFFRACTIONr_scbond_other1.4622.731666
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3953.9782398
X-RAY DIFFRACTIONr_long_range_B_refined4.8928.5163419
X-RAY DIFFRACTIONr_long_range_B_other4.81728.2023389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 180 -
Rwork0.268 3017 -
obs--99.69 %
Refinement TLS params.Method: refined / Origin x: -16.2392 Å / Origin y: -43.629 Å / Origin z: -0.2061 Å
111213212223313233
T0.0157 Å20.0162 Å20.005 Å2-0.1055 Å20.0418 Å2--0.0371 Å2
L0.5687 °2-0.6155 °2-0.0877 °2-1.0062 °20.2566 °2--0.6868 °2
S0.0449 Å °-0.0049 Å °0.0244 Å °-0.0315 Å °0.0161 Å °-0.056 Å °-0.0613 Å °-0.0042 Å °-0.061 Å °

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