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- PDB-5ezd: Crystal structure of a Hepatocyte growth factor activator inhibit... -

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Basic information

Entry
Database: PDB / ID: 5ezd
TitleCrystal structure of a Hepatocyte growth factor activator inhibitor-1 (HAI-1) fragment covering the PKD-like 'internal' domain and Kunitz domain 1
ComponentsKunitz-type protease inhibitor 1
KeywordsHYDROLASE / Transmembrane / multidomain / serine protease inhibitor / tertiary structure
Function / homology
Function and homology information


epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / epidermis development / extracellular matrix organization ...epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / epidermis development / extracellular matrix organization / neural tube closure / serine-type endopeptidase inhibitor activity / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / MANSC domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A ...MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / MANSC domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / : / Kunitz-type protease inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHong, Z. / Andreasen, P.A. / Morth, J.P. / Jensen, J.K.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Cancer SocietyNA Denmark
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Crystal Structure of a Two-domain Fragment of Hepatocyte Growth Factor Activator Inhibitor-1: FUNCTIONAL INTERACTIONS BETWEEN THE KUNITZ-TYPE INHIBITOR DOMAIN-1 AND THE NEIGHBORING POLYCYSTIC ...Title: Crystal Structure of a Two-domain Fragment of Hepatocyte Growth Factor Activator Inhibitor-1: FUNCTIONAL INTERACTIONS BETWEEN THE KUNITZ-TYPE INHIBITOR DOMAIN-1 AND THE NEIGHBORING POLYCYSTIC KIDNEY DISEASE-LIKE DOMAIN.
Authors: Hong, Z. / De Meulemeester, L. / Jacobi, A. / Pedersen, J.S. / Morth, J.P. / Andreasen, P.A. / Jensen, J.K.
History
DepositionNov 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kunitz-type protease inhibitor 1
B: Kunitz-type protease inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7666
Polymers33,5702
Non-polymers1964
Water1,13563
1
A: Kunitz-type protease inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8242
Polymers16,7851
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kunitz-type protease inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9424
Polymers16,7851
Non-polymers1573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.650, 75.140, 75.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 166:181 or resseq 189:202 or resseq 207:224 or resseq 233:304 )
211chain B and (resseq 166:181 or resseq 189:202 or resseq 207:224 or resseq 233:304 )

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Components

#1: Protein Kunitz-type protease inhibitor 1 / Hepatocyte growth factor activator inhibitor type 1 / HAI-1


Mass: 16784.799 Da / Num. of mol.: 2 / Fragment: UNP residues 168-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPINT1, HAI1, UNQ223/PRO256 / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: O43278
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 28% w/v PEG 2000 MME, 0.1 M sodium acetate pH 5.5, 0.2 M potassium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→53.17 Å / Num. obs: 19615 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rsym value: 0.029 / Net I/σ(I): 22.8 / Num. measured all: 104438
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ISL

4isl


Resolution: 2.1→24.143 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1792 4.95 %Random selection
Rwork0.2203 ---
obs0.2221 36191 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→24.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 10 63 2011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081980
X-RAY DIFFRACTIONf_angle_d1.1442660
X-RAY DIFFRACTIONf_dihedral_angle_d13.732736
X-RAY DIFFRACTIONf_chiral_restr0.039296
X-RAY DIFFRACTIONf_plane_restr0.006338
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A969X-RAY DIFFRACTIONPOSITIONAL
12B969X-RAY DIFFRACTIONPOSITIONAL0.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.1570.30861050.30532667X-RAY DIFFRACTION98
2.157-2.22040.28591670.28062678X-RAY DIFFRACTION99
2.2204-2.2920.35831330.28822645X-RAY DIFFRACTION99
2.292-2.37390.36841400.28542704X-RAY DIFFRACTION99
2.3739-2.46890.37931070.24922690X-RAY DIFFRACTION100
2.4689-2.58110.37151360.23732680X-RAY DIFFRACTION99
2.5811-2.7170.2451450.23512670X-RAY DIFFRACTION99
2.717-2.8870.28071240.23562682X-RAY DIFFRACTION99
2.887-3.10950.24671670.23352605X-RAY DIFFRACTION99
3.1095-3.42160.2161750.23012612X-RAY DIFFRACTION97
3.4216-3.91490.28271390.2012571X-RAY DIFFRACTION96
3.9149-4.92550.2421480.18932552X-RAY DIFFRACTION96
4.9255-24.14490.22231060.22142643X-RAY DIFFRACTION97
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)
19.45613.99247.10394.02772.05215.72380.2064-1.0236-0.32270.19910.4386-0.57430.03321.1139-0.52650.53090.0571-0.13430.9307-0.20720.74120.4983-0.203817.7941
21.86320.33110.06030.4433-0.20780.52150.07810.58710.1256-0.0814-0.04450.14610.0149-0.17140.57160.29-0.1080.22490.7883-0.43571.0226-12.9212-2.997715.8685
36.9326-2.36632.72555.3225-0.75712.3487-0.99580.10170.1049-0.7393-0.76590.5827-1.0366-1.69371.08780.70690.24-0.20541.1018-0.38231.5064-11.48029.673420.9436
42.34351.7418-2.74492.85470.91629.71740.2079-1.99410.31392.2188-0.86212.77150.172-0.79410.92370.9084-0.24560.15131.3219-0.34741.3628-15.415-2.9424.7808
57.5636-0.019-0.33495.21371.92344.4734-0.133-0.06741.1995-0.0577-0.56521.0073-0.8052-1.65110.39890.63410.08-0.11780.5973-0.09050.8136-7.43312.531814.124
64.10230.8725.50788.84052.33739.2235-0.29280.9827-0.4442-0.84630.4533-1.4543-0.14011.3674-0.28460.7135-0.06530.12080.841-0.07190.498211.6029-7.51211.3263
72.89-2.3261-0.83937.5036-0.33686.75240.09140.4463-0.924-0.76140.17291.01391.3828-0.2686-0.2740.8137-0.0039-0.04760.5061-0.04370.49721.7417-12.60394.1674
86.50251.291-5.61238.22880.98628.17030.2299-0.04150.4765-0.0969-0.09621.01440.0222-0.0976-0.20260.6113-0.1019-0.08190.5815-0.01560.5821-0.1302-7.19617.6226
93.35693.9078-1.09384.5601-1.06185.63520.3573-0.4112-0.3376-0.0535-0.83591.71920.3312-0.30930.29710.5269-0.08660.03330.6553-0.14480.996713.91821.01219.0256
101.43550.451-0.37670.18070.06310.94380.1776-0.03840.52450.01450.0115-0.1303-0.18210.1215-0.44730.31370.2139-0.03110.9618-0.46070.796627.33532.929321.8315
117.7777-0.9084-2.10132.8632-2.81913.9735-0.6730.38030.5318-0.82041.455-1.3112-0.58830.5597-0.68880.7164-0.33210.22791.6314-0.4371.139425.9003-2.12579.1501
122.3645-2.1382-0.03193.61260.75151.94150.17520.4488-2.4709-0.01770.333-0.58561.98713.1823-0.67040.96490.1247-0.22791.3957-0.27771.324529.8251-5.984521.7608
135.1967-1.04072.03246.78193.95547.2194-0.10681.1632-0.508-0.27711.0389-1.54520.36811.2525-0.82180.7244-0.02460.05881.2537-0.33090.843924.4894-1.457915.6667
144.8064-2.54750.59731.3581-0.12935.1918-0.12030.64511.0309-0.42250.0093-0.9108-1.07920.6321-0.09070.4553-0.15820.1110.4680.04040.428619.039111.224916.9818
156.88244.2628-0.10426.85071.897.9528-0.1038-0.40860.90010.2526-0.19760.8519-0.784-1.20270.21460.68930.1078-0.05320.4363-0.11510.86352.81317.469226.3556
167.1776-0.7125-0.86786.2030.618.2510.0371-0.74780.76221.3743-0.062-0.2597-0.73680.95650.15910.7919-0.0526-0.00710.39-0.02810.533212.667614.617431.4487
176.8853-5.392-0.04825.51391.26777.57850.19880.6712-0.02940.0169-0.1895-0.12-0.16591.06850.01740.6146-0.0935-0.11140.5303-0.01310.576614.541811.170326.0364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 166 through 173 )
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 189 )
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 198 )
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 208 )
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 250 )
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 262 )
7X-RAY DIFFRACTION7chain 'A' and (resid 263 through 280 )
8X-RAY DIFFRACTION8chain 'A' and (resid 281 through 304 )
9X-RAY DIFFRACTION9chain 'B' and (resid 166 through 173 )
10X-RAY DIFFRACTION10chain 'B' and (resid 174 through 189 )
11X-RAY DIFFRACTION11chain 'B' and (resid 190 through 198 )
12X-RAY DIFFRACTION12chain 'B' and (resid 199 through 208 )
13X-RAY DIFFRACTION13chain 'B' and (resid 209 through 233 )
14X-RAY DIFFRACTION14chain 'B' and (resid 234 through 250 )
15X-RAY DIFFRACTION15chain 'B' and (resid 251 through 262 )
16X-RAY DIFFRACTION16chain 'B' and (resid 263 through 280 )
17X-RAY DIFFRACTION17chain 'B' and (resid 281 through 304 )

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