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- PDB-6ht9: Mouse fetuin-B in complex with crayfish astacin -

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Basic information

Entry
Database: PDB / ID: 6ht9
TitleMouse fetuin-B in complex with crayfish astacin
Components
  • Astacin
  • Fetuin-B
KeywordsHYDROLASE / peptidase inhibitor / metallopeptidase / astacin / ovastacin inhibitor / fetuin / cystatin
Function / homology
Function and homology information


astacin / glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / metalloendopeptidase inhibitor activity / positive regulation of protein processing / binding of sperm to zona pellucida / negative regulation of endopeptidase activity ...astacin / glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / metalloendopeptidase inhibitor activity / positive regulation of protein processing / binding of sperm to zona pellucida / negative regulation of endopeptidase activity / fertilization / cysteine-type endopeptidase inhibitor activity / single fertilization / metalloendopeptidase activity / peptidase activity / cell adhesion / proteolysis / extracellular space / zinc ion binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proteinase inhibitor I25C, fetuin, conserved site / Fetuin-B-type cystatin domain / Fetuin family signature 1. / Fetuin family signature 2. / Fetuin-B-type cystatin domain profile. / Astacin-like metallopeptidase domain / : / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) ...Proteinase inhibitor I25C, fetuin, conserved site / Fetuin-B-type cystatin domain / Fetuin family signature 1. / Fetuin family signature 2. / Fetuin-B-type cystatin domain profile. / Astacin-like metallopeptidase domain / : / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Astacus astacus (noble crayfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGomis-Ruth, F.X. / Goulas, T. / Guevara, T. / Cuppari, A.
CitationJournal: Iucrj / Year: 2019
Title: Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition.
Authors: Cuppari, A. / Korschgen, H. / Fahrenkamp, D. / Schmitz, C. / Guevara, T. / Karmilin, K. / Kuske, M. / Olf, M. / Dietzel, E. / Yiallouros, I. / de Sanctis, D. / Goulas, T. / Weiskirchen, R. / ...Authors: Cuppari, A. / Korschgen, H. / Fahrenkamp, D. / Schmitz, C. / Guevara, T. / Karmilin, K. / Kuske, M. / Olf, M. / Dietzel, E. / Yiallouros, I. / de Sanctis, D. / Goulas, T. / Weiskirchen, R. / Jahnen-Dechent, W. / Floehr, J. / Stoecker, W. / Jovine, L. / Gomis-Ruth, F.X.
History
DepositionOct 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: 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
A: Astacin
B: Fetuin-B
C: Astacin
D: Fetuin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,46713
Polymers139,9714
Non-polymers1,4959
Water82946
1
A: Astacin
B: Fetuin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9738
Polymers69,9862
Non-polymers9876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-40 kcal/mol
Surface area25090 Å2
MethodPISA
2
C: Astacin
D: Fetuin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4945
Polymers69,9862
Non-polymers5083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-46 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.400, 85.800, 168.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Astacin / Crayfish small molecule proteinase


Mass: 28115.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Mature form spanning residues 50-251 plus a catalytic zinc ion.
Source: (natural) Astacus astacus (noble crayfish) / References: UniProt: P07584, astacin
#2: Protein Fetuin-B / Fetuin-like protein IRL685


Mass: 41870.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fetub / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9QXC1

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Sugars , 2 types, 4 molecules

#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.: 1
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
#6: 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.: 3
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

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Non-polymers , 3 types, 51 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: ammonium sulfate, polyethylene glycol 2000, sodium acetate, pH 4.6.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979182 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979182 Å / Relative weight: 1
ReflectionResolution: 3.1→84.4 Å / Num. obs: 22647 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 78.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.153 / Rrim(I) all: 0.16 / Net I/σ(I): 14.1
Reflection shellResolution: 3.1→3.28 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.499 / Mean I/σ(I) obs: 2 / CC1/2: 0.771 / Rrim(I) all: 1.567 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AST

1ast


Resolution: 3.1→34.12 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.882 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.49
RfactorNum. reflection% reflectionSelection details
Rfree0.27 643 2.84 %RANDOM
Rwork0.216 ---
obs0.217 22624 100 %-
Displacement parametersBiso mean: 101.22 Å2
Baniso -1Baniso -2Baniso -3
1--4.7691 Å20 Å20 Å2
2--4.9969 Å20 Å2
3----0.2278 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: 1 / Resolution: 3.1→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7899 0 90 46 8035
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018193HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1411162HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3692SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1392HARMONIC5
X-RAY DIFFRACTIONt_it8193HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion3.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1079SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance12HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9184SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.25 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3258 -3.31 %
Rwork0.2625 2865 -
all0.2646 2963 -
obs--100 %
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)
11.95280.93811.04645.83790.9164.070.07730.2381-0.02580.0642-0.1115-0.2223-0.1910.06290.0343-0.2981-0.0449-0.0228-0.11030.0365-0.283931.023513.605251.556
24.0581-2.91612.15473.7629-0.59580.71480.01620.3260.5029-0.14-0.09010.0333-0.2645-0.38530.0738-0.11320.14770.03960.26080.08670.0628-9.056120.072350.7201
35.442-2.79930.99130-3.20451.8711-0.05880.0323-0.1272-0.0341-0.07680.1593-0.1792-0.16980.1356-0.05930.0117-0.00470.0934-0.07280.040817.43089.461448.1372
46.77390.351-2.20595.5613-1.92496.8774-0.3789-0.2883-0.48150.22150.10710.0540.354-0.20160.27190.21960.0099-0.0256-0.1127-0.027-0.28477.3624-2.690566.4326
51.1858-2.09431.89535.15210.77681.53210.15530.84870.0815-0.54740.0021-0.1762-0.06970.1534-0.15740.04470.052-0.03560.56920.13390.2182-8.721217.350741.4016
65.25680.7490.573.06870.46053.963-0.08390.0387-0.46280.11710.0655-0.050.0097-0.05550.01840.1880.0261-0.0947-0.3226-0.0872-0.282347.749634.367875.5728
73.2267-3.2450.7514.7851-0.63061.473-0.4053-0.16810.06421.33090.28820.0796-1.0149-0.50130.11710.90470.18520.0043-0.2454-0.0016-0.229242.811974.617776.2569
80-1.3913-4.5261.93710.488900.00530.19540.3553-0.0140.0941-0.2567-0.38780.3518-0.09940.3470.1203-0.2125-0.0266-0.043-0.12852.242147.747178.895
92.8237-0.1297-0.99396.7655-2.80268.75080.01730.1718-0.062-0.0533-0.3837-0.63960.47540.88750.3665-0.08890.0349-0.05870.16150.0357-0.25963.653655.118459.9146
102.8648-0.2374-0.09692.4958-0.33850-0.0876-0.73330.12351.28490.09480.1412-0.5239-0.2241-0.00721.1940.1336-0.1273-0.1640.0428-0.082745.604577.283.4337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 202 A|999 - 999}
2X-RAY DIFFRACTION2{B|29 - 145 B|1001 - 1012}
3X-RAY DIFFRACTION3{B|146 - 160}
4X-RAY DIFFRACTION4{B|161 - 272}
5X-RAY DIFFRACTION5{B|303 - 388 B|501 - 502}
6X-RAY DIFFRACTION6{C|1 - 200 C|999 - 999}
7X-RAY DIFFRACTION7{D|28 - 145 D|1001 - 1011}
8X-RAY DIFFRACTION8{D|146 - 160}
9X-RAY DIFFRACTION9{D|161 - 267}
10X-RAY DIFFRACTION10{D|303 - 388 D|501 - 501}

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