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- PDB-5xrf: Crystal structure of Da-36, a thrombin-like enzyme from Deinagkis... -

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Basic information

Entry
Database: PDB / ID: 5xrf
TitleCrystal structure of Da-36, a thrombin-like enzyme from Deinagkistrodon acutus
ComponentsSnake venom serine protease Da-36
KeywordsHYDROLASE / thrombin-like enzyme / snake venom / Deinagkistrodon acutus
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
: / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan ...: / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Snake venom serine protease Da-36
Similarity search - Component
Biological speciesDeinagkistrodon acutus (Chinese moccasin)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLin, C.-C. / Wu, W.-G. / Fan, Q. / Tian, J. / Zhang, Z. / Zheng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Yunnan Provincial Science and Technology Department2013FA060 China
CitationJournal: To Be Published
Title: Crystal structure of Da-36, a thrombin-like enzyme from Deinagkistrodon acutus
Authors: Fan, Q. / Tian, J. / Zhang, Z. / Lin, C.-C. / Wu, W.-G. / Zheng, Y.
History
DepositionJun 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Nov 22, 2023Group: 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Snake venom serine protease Da-36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7934
Polymers27,0601
Non-polymers1,7343
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint29 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.481, 87.481, 104.674
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Snake venom serine protease Da-36


Mass: 27059.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: J7LCB0
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]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-1a_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)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.27 Å3/Da / Density % sol: 71.21 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.2M magnesium acetate tetrahydrate, 0.1M sodium cacodylate trihydrate pH 6.5, 20% polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23907 / % possible obs: 99.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 27.52
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 11 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 6.576 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GSO

4gso


Resolution: 2.2→37.88 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.61
RfactorNum. reflection% reflection
Rfree0.193 1284 5.42 %
Rwork0.179 --
obs0.184 23688 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 116 254 2219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062050
X-RAY DIFFRACTIONf_angle_d0.8432806
X-RAY DIFFRACTIONf_dihedral_angle_d15.4561238
X-RAY DIFFRACTIONf_chiral_restr0.044331
X-RAY DIFFRACTIONf_plane_restr0.004344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2006-2.28870.22531390.21112221X-RAY DIFFRACTION90
2.2887-2.39290.2381690.21182473X-RAY DIFFRACTION100
2.3929-2.5190.24711620.21692460X-RAY DIFFRACTION100
2.519-2.67680.23611290.20942505X-RAY DIFFRACTION100
2.6768-2.88340.23351230.21012510X-RAY DIFFRACTION100
2.8834-3.17350.21831340.19642532X-RAY DIFFRACTION100
3.1735-3.63230.1751420.17582525X-RAY DIFFRACTION100
3.6323-4.57510.18191420.14532543X-RAY DIFFRACTION100
4.5751-37.8860.17461440.17532635X-RAY DIFFRACTION99
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)
11.6721-0.05371.63111.116-1.03853.1049-0.0977-0.17690.0687-0.1905-0.158-0.18330.0938-0.04160.14350.2240.11370.01060.2062-0.01270.247912.930247.469641.9294
22.38430.0658-0.69060.8352-1.55013.01330.08160.1893-0.3051-0.4363-0.2246-0.41090.45320.53720.1630.30990.14930.10540.28240.05940.352220.115642.00238.0485
30.8192-0.049-0.56530.42320.1224.21240.06620.1116-0.206-0.4352-0.1947-0.16220.52830.1880.00220.39690.19120.06170.29470.00290.303414.941941.889336.87
40.9439-0.29890.72891.4573-0.1543.4596-0.0239-0.08540.0148-0.3806-0.1434-0.16710.2889-0.12310.12550.30460.11460.02060.1847-0.01680.21968.168148.177333.3033
51.0968-1.14071.52012.3031-0.43073.2945-0.36910.20150.4861-0.1234-0.2922-0.546-0.82640.41810.49740.40960.0489-0.13440.21660.0970.450216.55762.093333.1724
63.85620.87741.05064.36020.26973.357-0.03880.3852-0.0152-0.4076-0.2068-0.4220.09170.19760.17320.39570.14010.01190.19440.02440.208611.665751.622726.836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 25 THROUGH 65 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 66 THROUGH 77 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 78 THROUGH 107 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 108 THROUGH 148 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 149 THROUGH 207 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 208 THROUGH 260 )

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