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- PDB-4dur: The X-ray Crystal Structure of Full-Length type II Human Plasminogen -

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Basic information

Entry
Database: PDB / ID: 4dur
TitleThe X-ray Crystal Structure of Full-Length type II Human Plasminogen
ComponentsPlasminogen
KeywordsHYDROLASE / serine protease / fibrinolysis
Function / homology
Function and homology information


plasmin / tissue remodeling / protein antigen binding / Signaling by PDGF / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / Dissolution of Fibrin Clot / biological process involved in interaction with symbiont / Activation of Matrix Metalloproteinases / apolipoprotein binding ...plasmin / tissue remodeling / protein antigen binding / Signaling by PDGF / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / Dissolution of Fibrin Clot / biological process involved in interaction with symbiont / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / negative regulation of cell-substrate adhesion / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / : / endopeptidase activity / blood microparticle / protein domain specific binding / external side of plasma membrane / signaling receptor binding / negative regulation of cell population proliferation / serine-type endopeptidase activity / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain ...Peptidase S1A, plasmin / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Plasminogen Kringle 4 / Plasminogen Kringle 4 / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 3-Layer(bba) Sandwich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / 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 / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BICARBONATE ION / : / Plasminogen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLaw, R.H.P. / Caradoc-Davies, T. / Whisstock, J.C.
CitationJournal: Cell Rep / Year: 2012
Title: The X-ray crystal structure of full-length human plasminogen
Authors: Law, R.H.P. / Caradoc-Davies, T. / Cowieson, N. / Horvath, A.J. / Quek, A.J. / Encarnacao, J.A. / Steer, D. / Cowan, A. / Zhang, Q. / Lu, B.G.C. / Pike, R.N. / Smith, A.I. / Coughlin, P.B. / Whisstock, J.C.
History
DepositionFeb 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Structure summary
Revision 1.2Jun 26, 2013Group: Database references
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_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.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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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
Revision 2.2Oct 9, 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: Plasminogen
B: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,94616
Polymers177,0892
Non-polymers1,85714
Water25,8701436
1
A: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5209
Polymers88,5441
Non-polymers9768
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4267
Polymers88,5441
Non-polymers8816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.620, 144.620, 233.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Plasminogen / serine protease


Mass: 88544.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: plasma / References: UniProt: P00747, plasmin
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1448 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1436 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.98 Å3/Da / Density % sol: 69.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate, 0.2M sodium acetate, polyethylene glycol 1000, polyethylene glycol 8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953692 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 4, 2011 / Details: Silicon mirrors (adaptive and U-bent)
RadiationMonochromator: Double crystal monochromator (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953692 Å / Relative weight: 1
ReflectionResolution: 2.45→125.25 Å / Num. obs: 104073 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.9 % / Biso Wilson estimate: 43.58 Å2 / Rmerge(I) obs: 0.175 / Rsym value: 0.071 / Net I/σ(I): 9.2
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 2.3 / Num. unique all: 79752 / Rsym value: 0.351 / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QRZ, 1KRN, 5HPG, 1LOS

1qrz

1krn

5hpg

1los


Resolution: 2.45→125.25 Å / Cor.coef. Fo:Fc: 0.9197 / Cor.coef. Fo:Fc free: 0.8979 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.188 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 5236 5.03 %RANDOM
Rwork0.1897 ---
obs0.191 104035 99.8 %-
Displacement parametersBiso max: 147.84 Å2 / Biso mean: 34.1888 Å2 / Biso min: 8.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.7801 Å20 Å20 Å2
2---2.7801 Å20 Å2
3---5.5603 Å2
Refine analyzeLuzzati coordinate error obs: 0.283 Å
Refinement stepCycle: LAST / Resolution: 2.45→125.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11671 0 111 1436 13218
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4039SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes289HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1772HARMONIC5
X-RAY DIFFRACTIONt_it12189HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1582SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14253SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12189HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg16636HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.07
X-RAY DIFFRACTIONt_other_torsion17.54
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 361 4.89 %
Rwork0.2304 7020 -
all0.2309 7381 -
obs--99.8 %
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)
10.30230.0516-0.10930.2258-0.07980.04550.0218-0.00790.0534-0.02170.0130.0281-0.06230.0203-0.0349-0.01270.0009-0.0068-0.0374-0.0063-0.0445-72.500465.929613.3602
20.1609-0.0094-0.0430.09050.02510.3202-0.01370.0096-0.03210.023-0.0370.0030.0332-0.07350.0507-0.0413-0.0099-0.0020.0052-0.0093-0.043-16.036757.5692-20.1826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|791 A|801 - A|810 A|901 - A|1635 }A3 - 791
2X-RAY DIFFRACTION1{ A|3 - A|791 A|801 - A|810 A|901 - A|1635 }A801 - 810
3X-RAY DIFFRACTION1{ A|3 - A|791 A|801 - A|810 A|901 - A|1635 }A901 - 1635
4X-RAY DIFFRACTION2{ B|2 - B|791 B|801 - B|808 B|901 - B|1601 }B2 - 791
5X-RAY DIFFRACTION2{ B|2 - B|791 B|801 - B|808 B|901 - B|1601 }B801 - 808
6X-RAY DIFFRACTION2{ B|2 - B|791 B|801 - B|808 B|901 - B|1601 }B901 - 1601

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