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- PDB-4a5t: STRUCTURAL BASIS FOR THE CONFORMATIONAL MODULATION -

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Basic information

Entry
Database: PDB / ID: 4a5t
TitleSTRUCTURAL BASIS FOR THE CONFORMATIONAL MODULATION
ComponentsPLASMINOGENPlasmin
KeywordsHYDROLASE / MULTI-DOMAIN CONFORMATIONAL CHANGE
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / negative regulation of cell-cell adhesion mediated by cadherin / Signaling by PDGF / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / 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 / Schaffer collateral - CA1 synapse / 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 / collagen-containing extracellular matrix / blood microparticle / endopeptidase activity / protease binding / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / 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 / Kringle 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsXue, Y. / Bodin, C. / Olsson, K.
CitationJournal: J. Thromb. Haemost. / Year: 2012
Title: Crystal Structure of the Native Plasminogen Reveals an Activation-Resistant Compact Conformation.
Authors: Xue, Y. / Bodin, C. / Olsson, K.
History
DepositionOct 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Jul 18, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_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_database_status.status_code_sf / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "SH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "SH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "SI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: PLASMINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2904
Polymers88,5441
Non-polymers7463
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.460, 118.460, 179.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PLASMINOGEN / Plasmin / PLASMIN HEAVY CHAIN A / ACTIVATION PEPTIDE / ANGIOSTATIN / PLASMIN HEAVY CHAIN A\ / SHORT FORM / ...PLASMIN HEAVY CHAIN A / ACTIVATION PEPTIDE / ANGIOSTATIN / PLASMIN HEAVY CHAIN A\ / SHORT FORM / PLASMIN LIGHT CHAIN B


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


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-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-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.27 % / Description: NONE

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.49→75 Å / Num. obs: 16059 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 13.1 % / Biso Wilson estimate: 63.65 Å2 / Rmerge(I) obs: 0.27 / Net I/σ(I): 10.3
Reflection shellResolution: 3.49→3.58 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.49→50.8 Å / Cor.coef. Fo:Fc: 0.8731 / Cor.coef. Fo:Fc free: 0.8237 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.541
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL SIA GAL NGA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6026. NUMBER WITH APPRO APPROX DEFAULT CCP4 ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL SIA GAL NGA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6026. NUMBER WITH APPRO APPROX DEFAULT CCP4 ATOM TYPE=45. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 811 5.05 %RANDOM
Rwork0.2085 ---
obs0.2106 16059 95.29 %-
Displacement parametersBiso mean: 98.58 Å2
Baniso -1Baniso -2Baniso -3
1-13.576 Å20 Å20 Å2
2--13.576 Å20 Å2
3----27.1519 Å2
Refine analyzeLuzzati coordinate error obs: 0.754 Å
Refinement stepCycle: LAST / Resolution: 3.49→50.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6026 0 47 0 6073
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086271HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.158549HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2166SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes157HARMONIC2
X-RAY DIFFRACTIONt_gen_planes902HARMONIC5
X-RAY DIFFRACTIONt_it6271HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion22.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion805SEMIHARMONIC5
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_contact6959SEMIHARMONIC4
LS refinement shellResolution: 3.49→3.73 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2802 139 4.91 %
Rwork0.2417 2691 -
all0.2436 2830 -
obs--95.29 %
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)
13.0606-0.7592-2.48475.09940.19872.00140.0488-0.42430.23180.5011-0.0630.0964-0.26530.27870.01420.0674-0.0550.05750.1078-0.1187-0.125113.223830.0227.7387
27.99934.1421-3.36448.2128-2.48312.04120.036-0.09930.1621-0.2368-0.2463-0.0622-0.11220.12830.21030.0840.07430.2421-0.06120.0223-0.18325.614743.6033-12.3087
34.87480.24510.73114.1156-1.30572.56610.03910.37510.72650.3515-0.10560.0099-0.0034-0.16890.0665-0.23530.22340.1543-0.0103-0.10680.0952-8.886746.6683-5.1449
41.8022-1.37580.27260.05112.427100.01260.0378-0.0015-0.1806-0.0083-0.01350.0980.0142-0.0042-0.2460.1543-0.13310.1399-0.02210.07114.111939.924-25.2098
55.2756-0.35144.85570.38080.35120.8826-0.03130.30470.0003-0.2834-0.0263-0.0274-0.12340.02540.0576-0.16550.3941-0.08990.78520.085-0.0207-12.595244.1961-32.5503
61.79580.54631.05250-2.577600.02060.15360.0194-0.4276-0.05360.1822-0.02850.07980.033-0.1967-0.0840.10740.1818-0.28350.1949-6.616622.4747-21.5536
72.1420.7705-0.33150.1230.67480.7035-0.02630.1875-0.3440.0686-0.40960.38660.1733-0.51020.4359-0.0306-0.04860.14910.1393-0.28090.0682-4.693214.1693-1.0745
86.2729-2.62390.33253.89610.63473.3567-0.3309-0.425-0.2770.17070.0662-0.18090.3674-0.0370.26470.0061-0.09470.25460.0309-0.1689-0.1381-1.513914.240623.6354
93.02130.23040.63323.58020.6451.1703-0.03240.9589-0.2211-0.15-0.18760.5872-0.0043-0.95610.22-0.49130.01950.08940.6132-0.42550.1199-35.312626.3309-4.4435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN S AND RESID 1-82)
2X-RAY DIFFRACTION2(CHAIN S AND RESID 83-163)
3X-RAY DIFFRACTION3(CHAIN S AND RESID 164-244)
4X-RAY DIFFRACTION4(CHAIN S AND RESID 245-254)
5X-RAY DIFFRACTION5(CHAIN S AND RESID 255-334)
6X-RAY DIFFRACTION6(CHAIN S AND RESID 335-351)
7X-RAY DIFFRACTION7(CHAIN S AND RESID 352-435)
8X-RAY DIFFRACTION8(CHAIN S AND RESID 460-543)
9X-RAY DIFFRACTION9(CHAIN S AND RESID 544-791)

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