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- PDB-2bdz: Mexicain from Jacaratia mexicana -

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Basic information

Entry
Database: PDB / ID: 2bdz
TitleMexicain from Jacaratia mexicana
ComponentsMexicain
KeywordsHYDROLASE / mexicain / Cysteine protease / Peptidase_C1 / papain-like
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region
Similarity search - Function
Papain-like cysteine endopeptidase / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. ...Papain-like cysteine endopeptidase / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesJacaratia mexicana (bonete)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsGavira, J.A. / Oliver-Salvador, M.C. / Gonzalez-Ramirez, L.A. / Soriano-Garcia, M. / Garcia-Ruiz, J.M.
Citation
Journal: To be Published
Title: Crystallographic structure of Mexicain from Jacaratia mexicana
Authors: Gavira, J.A. / Oliver-Salvador, M.C. / Gonzalez-Ramirez, L.A. / Soriano-Garcia, M. / Garcia-Ruiz, J.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray analysis of Mexicain
Authors: Oliver-Salvador, M.C. / Gonzalez-Ramirez, L.A. / Gavira, J.A. / Soriano-Garcia, M. / Garcia-Ruiz, J.M.
History
DepositionOct 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Aminoacids R58 and T70 appear in the deposited sequence P84346 (name: MEX1_JACME) of the ...SEQUENCE Aminoacids R58 and T70 appear in the deposited sequence P84346 (name: MEX1_JACME) of the SWS data base as Y58 and P70 respectively but there are clear evidences for the current substitutions pointing to sequenciation errors.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mexicain
B: Mexicain
C: Mexicain
D: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6178
Polymers95,1754
Non-polymers1,4424
Water6,828379
1
A: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1542
Polymers23,7941
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1542
Polymers23,7941
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1542
Polymers23,7941
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mexicain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1542
Polymers23,7941
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.356, 90.454, 80.391
Angle α, β, γ (deg.)90.00, 92.636, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is the monomer. The asymetric unit contains four biological units named A,B,C and D.

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Components

#1: Protein
Mexicain


Mass: 23793.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: latex / Source: (natural) Jacaratia mexicana (bonete)
References: UniProt: P84346, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 20 % (w/v) PEGl 6000, 0.1 M citrate, 15 % (v/v) ethanolamine, pH 10.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER / Wavelength: 1.5418
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Sep 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40.8 Å / Num. obs: 47249 / % possible obs: 99.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.095 / Χ2: 3.115 / Net I/σ(I): 17.271
Reflection shellResolution: 2.1→2.18 Å / % possible obs: 97.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.495 / Num. measured obs: 4587 / Χ2: 1.694 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0005refinement
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACT1.6data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, ...Starting model: The initial model was calculated using the SWISS-MODEL server using ProModII for modelling and GROMOS96 for energy minimization (Schwede et al., 2000). Initial models pdb I.Ds.: 1yal, 1gec, 1ppo, 1meg and 1pci

1yal

1gec

1ppo

1meg

1pci


Resolution: 2.1→40.8 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.066 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: MolProbity, XtalView were also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 4576 10 %RANDOM
Rwork0.177 ---
all0.183 ---
obs-40977 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.046 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.27 Å2
2--1.05 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 100 379 6951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226786
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.969206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38823.958283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.555151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8471536
X-RAY DIFFRACTIONr_chiral_restr0.0690.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025166
X-RAY DIFFRACTIONr_nbd_refined0.2030.23462
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2607
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.218
X-RAY DIFFRACTIONr_mcbond_it1.23524312
X-RAY DIFFRACTIONr_mcangle_it1.81936742
X-RAY DIFFRACTIONr_scbond_it1.322900
X-RAY DIFFRACTIONr_scangle_it1.80132464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.103-2.1580.2972950.1892707350885.576
2.158-2.2170.2633150.1822739341689.403
2.217-2.2810.2642890.1782794335591.893
2.281-2.3520.2573020.1822687320393.319
2.352-2.4290.2613050.1832666314494.497
2.429-2.5140.2682870.1852614303495.616
2.514-2.6090.2492920.1892527293995.917
2.609-2.7150.2752790.1962424279696.674
2.715-2.8360.2322680.1882393272097.831
2.836-2.9740.2562740.1732268258498.375
2.974-3.1340.2272500.182163245098.49
3.134-3.3240.2292350.1732086233699.358
3.324-3.5530.2022120.1711969219699.317
3.553-3.8370.2192000.1571849205599.708
3.837-4.2030.181890.1541681187699.68
4.203-4.6970.2221620.151549171399.883
4.697-5.4210.2261500.1671353150699.801
5.421-6.6310.2391310.2051144127999.687
6.631-9.3460.195950.167909100899.603
9.346-80.3220.3460.27545557686.979

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