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- PDB-6f02: Crystal structure of human glycosylated kallistatin at 3.0 Angstr... -

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Basic information

Entry
Database: PDB / ID: 6f02
TitleCrystal structure of human glycosylated kallistatin at 3.0 Angstrom resolution
ComponentsKallistatin
KeywordsHYDROLASE / Serine protease inhibitor / kallilrein / protease / inhibitor / heparin
Function / homology
Function and homology information


platelet dense granule lumen / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhou, A. / Ma, L.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
British Heart Foundation United Kingdom
NSFC81572090 China
Citation
Journal: To Be Published
Title: Crystal structure of human Kallistatin
Authors: Zhou, A. / Ma, L.
#1: Journal: To Be Published
Title: Structure of human native Kallistatin
Authors: zhou, A. / Ma, L.
History
DepositionNov 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kallistatin
C: Kallistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9488
Polymers89,1912
Non-polymers2,7586
Water362
1
A: Kallistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0613
Polymers44,5951
Non-polymers1,4652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Kallistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8875
Polymers44,5951
Non-polymers1,2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.020, 138.020, 157.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 44595.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: human Kallistatin was expressed in HEK293 cells with a His6-Tag at the C-terminus
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA4, KST, PI4 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P29622
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1b_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 293 K / Method: microbatch / Details: PEG3350, Salt

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3→104.15 Å / Num. obs: 29350 / % possible obs: 94.6 % / Redundancy: 5.7 % / Net I/σ(I): 9.4
Reflection shellResolution: 3→3.18 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4755 / CC1/2: 0.717 / Rpim(I) all: 0.548 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QLP

1qlp


Resolution: 3→104.15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.871 / SU B: 51.794 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R: 1.051 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27551 1430 4.9 %RANDOM
Rwork0.23362 ---
obs0.2357 27826 93.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.632 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å2-0 Å2-0 Å2
2--1.74 Å2-0 Å2
3----3.47 Å2
Refinement stepCycle: 1 / Resolution: 3→104.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6017 0 181 2 6200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196374
X-RAY DIFFRACTIONr_bond_other_d0.0020.025926
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9938653
X-RAY DIFFRACTIONr_angle_other_deg0.835313769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73423.441279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4671534
X-RAY DIFFRACTIONr_chiral_restr0.0630.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021326
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_it0.7895.2342981
X-RAY DIFFRACTIONr_mcbond_other0.7895.2332980
X-RAY DIFFRACTIONr_mcangle_it1.467.8463721
X-RAY DIFFRACTIONr_mcangle_other1.467.8473722
X-RAY DIFFRACTIONr_scbond_it0.6575.3573392
X-RAY DIFFRACTIONr_scbond_other0.6555.3573392
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2498.0224933
X-RAY DIFFRACTIONr_long_range_B_refined2.99359.1666489
X-RAY DIFFRACTIONr_long_range_B_other2.99359.1666489
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 106 -
Rwork0.378 2054 -
obs--96.34 %
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)
10.47870.4408-0.57880.9787-0.81551.71460.03440.0247-0.0180.0616-0.0561-0.0656-0.0177-0.00620.02170.5584-0.0036-0.05570.4382-0.02850.064841.5246135.924831.5043
20.6119-0.2674-0.47011.06811.30992.17130.03170.0231-0.0314-0.0922-0.007-0.0862-0.189-0.1243-0.02480.726-0.0042-0.0540.43860.0460.032446.318177.236833.3988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 1008
2X-RAY DIFFRACTION2C45 - 508

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