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- PDB-1cqd: THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SP... -

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Basic information

Entry
Database: PDB / ID: 1cqd
TitleTHE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SPECIFICITY FROM GINGER RHIZOME, ZINGIBER OFFICINALE
ComponentsPROTEIN (PROTEASE II)
KeywordsHYDROLASE / CYSTEINE PROTEASE / GLYCOPROTEIN / PROLINE SPECIFICITY / CARBOHYDRATE / PAPAIN FAMILY
Function / homology
Function and homology information


zingipain / cysteine-type peptidase activity / proteolysis
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
THIOSULFATE / Zingipain-2
Similarity search - Component
Biological speciesZingiber officinale (ginger)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChoi, K.H. / Laursen, R.A. / Allen, K.N.
CitationJournal: Biochemistry / Year: 1999
Title: The 2.1 A structure of a cysteine protease with proline specificity from ginger rhizome, Zingiber officinale.
Authors: Choi, K.H. / Laursen, R.A. / Allen, K.N.
History
DepositionJun 15, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 28, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / database_PDB_caveat / 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_chiral / 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_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _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
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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 / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PROTEASE II)
B: PROTEIN (PROTEASE II)
C: PROTEIN (PROTEASE II)
D: PROTEIN (PROTEASE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,14114
Polymers95,7654
Non-polymers3,37610
Water6,720373
1
A: PROTEIN (PROTEASE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0484
Polymers23,9411
Non-polymers1,1073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (PROTEASE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8454
Polymers23,9411
Non-polymers9043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (PROTEASE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6243
Polymers23,9411
Non-polymers6832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PROTEIN (PROTEASE II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6243
Polymers23,9411
Non-polymers6832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.980, 45.450, 110.040
Angle α, β, γ (deg.)90.00, 105.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99959, 0.02857, 0.00297), (0.02856, 0.99959, -0.00108), (-0.003, -0.00099, -0.99999)3.36429, 1.04461, 159.70383
2given(-0.78773, 0.01411, -0.61586), (0.01911, 0.99982, -0.00155), (0.61572, -0.01299, -0.78786)76.65181, -2.54158, 128.41476
3given(0.78446, 0.00146, 0.62018), (-0.00744, 0.99995, 0.00705), (-0.62013, -0.01014, 0.78443)-73.05138, -2.73918, 32.1021

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PROTEIN (PROTEASE II)


Mass: 23941.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PURIFIED FROM GROUND GINGER ROOT / Source: (natural) Zingiber officinale (ginger) / References: UniProt: P82474

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Sugars , 4 types, 6 molecules

#2: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 2 types, 377 molecules

#5: Chemical
ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O3S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHIOSULFATE IS ATTACHED TO CYS-27 IN ALL FOUR MONOMERS
Sequence detailsTHE SEQUENCE IS TO BE PUBLISHED IN A SEQUENCE DATABASE.

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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: 2.19 Å3/Da / Density % sol: 43.38 %
Description: INITIAL MODEL WAS GENERATED FROM PAPAIN, ACTINIDIN AND PROTEASE OMEGA BY SWISS- MODEL PROTEIN MODELING SERVER
Crystal growpH: 5.2
Details: 0.1 M SODIUM ACETATE BUFFER (PH 5.2) CONTAINING 0.1 M AMMONIUM SULFATE, 26% POLYETHYLENE GLYCOL MONOMETHYLETHER 2000, AND 2.5 MM SODIUM TETRATHIONATE
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
226 %mPEG20001reservoir
30.2 Mammonium sulfate1reservoir
40.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 15, 1997 / Details: SUPPER LONG MIRRORS
RadiationMonochromator: SUPPER LONG MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 58449 / % possible obs: 99.7 % / Redundancy: 5 % / Rsym value: 0.191 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.8 / % possible all: 75
Reflection
*PLUS
Rmerge(I) obs: 0.191
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 4505 10 %RANDOM
Rwork0.213 ---
obs0.213 48814 91.7 %-
Displacement parametersBiso mean: 13.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 214 373 7171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.06
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.527
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.291 506 7.7 %
Rwork0.251 4431 -
obs--75.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3TIP3P.PARTIP3P.TOP
X-RAY DIFFRACTION4S2O3.PARS2O3.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.214 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.527

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