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- PDB-4eb1: Hyperstable in-frame insertion variant of antithrombin -

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Basic information

Entry
Database: PDB / ID: 4eb1
TitleHyperstable in-frame insertion variant of antithrombin
Components(Antithrombin-III) x 2
KeywordsBLOOD CLOTTING / serpin / hydrolase inhibitor
Function / homology
Function and homology information


regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / collagen-containing extracellular matrix / protease binding ...regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / collagen-containing extracellular matrix / protease binding / blood microparticle / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Antithrombin-III, serpin domain / 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 ...Antithrombin-III, serpin domain / 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: 2.8 Å
AuthorsMartinez-Martinez, I. / Johnson, D.J.D. / Yamasaki, M. / Corral, J. / Huntington, J.A.
CitationJournal: J.Thromb.Haemost. / Year: 2012
Title: Type II antithrombin deficiency caused by a large in-frame insertion: structural, functional and pathological relevance.
Authors: Martinez-Martinez, I. / Johnson, D.J. / Yamasaki, M. / Navarro-Fernandez, J. / Ordonez, A. / Vicente, V. / Huntington, J.A. / Corral, J.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
I: Antithrombin-III
L: Antithrombin-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3196
Polymers99,0282
Non-polymers1,2914
Water48627
1
I: Antithrombin-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7944
Polymers49,9271
Non-polymers8673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: Antithrombin-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5252
Polymers49,1011
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.750, 101.750, 88.810
Angle α, β, γ (deg.)90.00, 105.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Antithrombin-III / ATIII / Serpin C1


Mass: 49927.031 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: S137A, E210del, L211del, insert VLVLVNTRTS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINC1, AT3, PRO0309 / Cell line (production host): HEK-EBNA / Production host: Homo sapiens (human) / References: UniProt: P01008
#2: Protein Antithrombin-III / latent alpha antithrombin / ATIII / Serpin C1


Mass: 49101.016 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-464 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: plasma / References: UniProt: P01008
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A IS AN ANTITHROMBIN VARIANT COMPRISING UNP RESIDUES 33-464 WITH UNP RESIDUES E241 AND L242 ...CHAIN A IS AN ANTITHROMBIN VARIANT COMPRISING UNP RESIDUES 33-464 WITH UNP RESIDUES E241 AND L242 REPLACED BY A VLVLVNTRTS INSERTION.

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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: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 17.0% PEG4000, 50 mM sodium/potassium phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.8→61.4 Å / Num. all: 29504 / Num. obs: 28324 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 82.014 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 10.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 0.18 / Num. unique all: 4144 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0098refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E04, CHAIN L

1e04


Resolution: 2.8→61.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 29.51 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.994 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25455 1426 5 %RANDOM
Rwork0.19764 ---
all0.20053 28077 --
obs0.20053 26872 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.203 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å2-3.33 Å2
2--2.99 Å2-0 Å2
3----3.42 Å2
Refinement stepCycle: LAST / Resolution: 2.8→61.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 84 27 6205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0226310
X-RAY DIFFRACTIONr_angle_refined_deg0.6251.9768580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0565793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8524.566265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54615981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4151529
X-RAY DIFFRACTIONr_chiral_restr0.0440.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214748
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 100 -
Rwork0.316 1983 -
obs-2083 97.7 %
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)
12.52143.1384-0.99153.9252-1.24490.4027-0.31490.2764-0.4622-0.15950.2756-0.6093-0.0103-0.17050.03930.60660.23560.00770.50640.00010.297974.458812.589335.9594
20.30440.2619-0.07370.48870.09550.55530.0246-0.0362-0.0376-0.0625-0.0527-0.1174-0.0035-0.00870.02810.24960.0197-0.03240.32320.01020.261464.39793.624946.7325
30.43920.32730.3151.9281-0.50241.82410.1774-0.0509-0.03820.0144-0.17020.2235-0.3828-0.0813-0.00730.3369-0.0146-0.0440.2759-0.01660.248658.370520.762751.6949
40.22220.088-0.38460.0838-0.21510.75560.0329-0.0551-0.03820.10420.00220.0505-0.23710.0732-0.03510.38170.0149-0.07780.31960.01220.272756.971512.974853.9978
50.59830.05980.06880.4522-0.07870.53270.0592-0.05710.0085-0.1033-0.070.03240.1437-0.08320.01080.32020.0124-0.06570.3301-0.02320.199842.4437-11.886541.6356
60.37250.25030.46760.5610.14480.67910.071-0.091-0.0030.0545-0.1051-0.01520.0302-0.05510.03410.28540.0121-0.05060.35-0.02280.219749.385-1.357848.6149
711.74992.74296.78253.6158-2.05458.4513-1.9935-1.31780.84590.10970.9825-0.2118-1.9062-2.57291.0110.50650.6454-0.26621.1811-0.39150.1485-8.75214.9179-0.5395
81.87260.12582.66880.19850.21993.8442-0.0143-0.08960.0795-0.0159-0.0513-0.0087-0.007-0.21830.06560.2634-0.0302-0.05650.342-0.00260.1734.4685-7.45820.1373
91.07670.22091.9230.51430.45034.35750.15940.3686-0.0230.2760.0779-0.15910.21390.2832-0.23720.23580.0631-0.11110.3933-0.01080.199927.8641-8.170223.0235
101.25660.07951.9860.16090.30543.90970.0561-0.13610.04010.05410.0053-0.05170.2878-0.2629-0.06140.2768-0.0516-0.07510.32170.02040.172310.028-9.399312.6505
110.51680.04842.06070.02460.16428.2690.18570.1625-0.0566-0.06370.0542-0.00480.80920.5632-0.23990.42130.0191-0.0880.339-0.04220.254312.4912-14.47182.8534
121.9825-0.87772.67250.8027-0.71864.1253-0.0581-0.11850.13860.1206-0.0586-0.14080.0267-0.29970.11670.3023-0.0091-0.06850.3553-0.00830.249614.7422-6.052715.2243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1I5 - 22
2X-RAY DIFFRACTION2I23 - 159
3X-RAY DIFFRACTION3I160 - 195
4X-RAY DIFFRACTION4I200 - 228
5X-RAY DIFFRACTION5I229 - 327
6X-RAY DIFFRACTION6I328 - 440
7X-RAY DIFFRACTION7L7 - 46
8X-RAY DIFFRACTION8L47 - 229
9X-RAY DIFFRACTION9L230 - 267
10X-RAY DIFFRACTION10L268 - 377
11X-RAY DIFFRACTION11L378 - 405
12X-RAY DIFFRACTION12L406 - 430

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