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- PDB-4d3x: The structure of mature legumain from chinese hamster. -

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Basic information

Entry
Database: PDB / ID: 4d3x
TitleThe structure of mature legumain from chinese hamster.
ComponentsLEGUMAINAsparagine endopeptidase
KeywordsHYDROLASE / CYSTEINE PROTEASE
Function / homology
Function and homology information


negative regulation of ERBB signaling pathway / legumain / renal system process / receptor catabolic process / self proteolysis / positive regulation of endothelial cell chemotaxis / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / negative regulation of multicellular organism growth ...negative regulation of ERBB signaling pathway / legumain / renal system process / receptor catabolic process / self proteolysis / positive regulation of endothelial cell chemotaxis / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / proteolysis involved in protein catabolic process / lysosomal lumen / positive regulation of mitotic cell cycle / positive regulation of long-term synaptic potentiation / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / negative regulation of neuron apoptotic process / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / extracellular region
Similarity search - Function
: / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family / Rossmann fold - #1460 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCRICETULUS GRISEUS (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 Å
AuthorsLi, W. / Heinz, D.W. / Krausze, J.
CitationJournal: To be Published
Title: A Detailed Look Into Chinese Hamster Legumain Active Site Structure and Exploration of its Function
Authors: Li, W. / Damme, M. / Buessow, K. / Grimm, I. / Van Den Heuvel, J. / Heinz, D.W. / Krausze, J.
History
DepositionOct 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEGUMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6413
Polymers32,1991
Non-polymers4422
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.620, 43.620, 209.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein LEGUMAIN / Asparagine endopeptidase


Mass: 32198.957 Da / Num. of mol.: 1 / Fragment: ASPARAGINYL ENDOPEPTIDASE DOMAIN, RESIDUES 31-314 / Source method: isolated from a natural source / Source: (natural) CRICETULUS GRISEUS (Chinese hamster) / Cell line: LEC3.8.2.1 / Organ: OVARY / References: UniProt: G3I1H5, legumain
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.79 Å3/Da / Density % sol: 31.5 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M NACL, 23%(W/V) PEG 3350, 0.1 M MOPS PH 6.5; THEN 10%(V/V) GLYCEROL WERE ADDED FOR CRYO-PROTECTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.84402
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.84402 Å / Relative weight: 1
ReflectionResolution: 1.85→38 Å / Num. obs: 33931 / % possible obs: 88.7 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 18.42 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.8
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 4.7 / % possible all: 19.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AWA

4awa


Resolution: 1.848→37.776 Å / SU ML: 0.23 / σ(F): 1.59 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 1687 5 %
Rwork0.1737 --
obs0.1767 33928 88.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 1.848→37.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 28 146 2267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072200
X-RAY DIFFRACTIONf_angle_d1.0612987
X-RAY DIFFRACTIONf_dihedral_angle_d15.773794
X-RAY DIFFRACTIONf_chiral_restr0.043315
X-RAY DIFFRACTIONf_plane_restr0.005386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8484-1.90280.3249360.2933681X-RAY DIFFRACTION22
1.9028-1.96420.3412960.25041867X-RAY DIFFRACTION63
1.9642-2.03440.32571350.23662574X-RAY DIFFRACTION86
2.0344-2.11580.32981530.2342929X-RAY DIFFRACTION97
2.1158-2.21210.231620.21263050X-RAY DIFFRACTION99
2.2121-2.32870.29471540.18782988X-RAY DIFFRACTION100
2.3287-2.47460.27021560.20093013X-RAY DIFFRACTION100
2.4746-2.66560.22051620.18583028X-RAY DIFFRACTION100
2.6656-2.93380.26331590.18923043X-RAY DIFFRACTION100
2.9338-3.35810.22011600.17283042X-RAY DIFFRACTION100
3.3581-4.22990.1731580.12853001X-RAY DIFFRACTION100
4.2299-37.78390.18051560.12963025X-RAY DIFFRACTION100
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)
10.475-0.06190.05220.5213-0.22190.66410.05780.04010.0553-0.04030.00530.0381-0.0472-0.0593-0.01180.1370.06130.03270.09530.0810.1052-52.044623.4954-19.2768
20.08740.1439-0.20490.5441-0.4570.75040.02370.0380.0368-0.0187-0.0191-0.0317-0.0455-0.0209-0.04720.24170.12890.11230.21990.12160.2154-51.971135.6923-26.5749
31.0322-0.0906-0.24350.6611-0.30640.65080.0357-0.01150.0489-0.0468-0.0265-0.0405-0.0433-0.0534-0.00190.15330.10910.06280.25830.11340.1782-55.245127.9897-23.366
41.18620.24150.32071.03440.06950.62890.0058-0.0107-0.0029-0.02010.06840.15440.0035-0.1976-0.04570.10230.02570.01370.3740.17230.2189-66.637620.2251-10.6261
51.3615-0.22830.87740.5186-0.62381.42650.0571-0.0017-0.0803-0.05920.03290.17210.0586-0.1643-0.1030.204-0.1045-0.11360.34490.14560.3192-63.465513.4092-15.2364
60.603-0.2351-0.06881.56760.40530.98350.0045-0.07430.07660.1530.0670.1227-0.2414-0.1891-0.00160.19220.07350.0360.09310.03340.1116-55.406228.4801-8.605
70.80110.2752-0.35740.5523-0.60441.21310.0973-0.1538-0.00030.18370.02720.1521-0.1788-0.1713-0.0270.1076-0.0341-0.00160.18130.09040.1285-54.422920.4531-1.3188
80.37590.1788-0.10231.383-0.11920.53970.0630.06080.1674-0.0316-0.0299-0.0049-0.27270.1071-0.13810.2322-0.07360.01640.21060.15880.2774-41.873133.7168-16.0013
91.04970.15-0.31290.5730.27980.6529-0.01570.0180.0248-0.0186-0.0126-0.1106-0.04080.1572-0.03810.0928-0.0408-0.01960.30990.16610.2299-35.855718.1899-9.5609
100.3158-0.20250.22980.8011-0.59561.3522-0.0206-0.03970.009-0.0018-0.104-0.1165-0.02260.1486-0.03710.1036-0.0284-0.0510.14860.12020.1963-42.684616.9136-6.3511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 32 THROUGH 74 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 75 THROUGH 94 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 95 THROUGH 114 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 115 THROUGH 129 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 130 THROUGH 144 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 145 THROUGH 164 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 165 THROUGH 218 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 219 THROUGH 248 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 249 THROUGH 266 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 267 THROUGH 292 )

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