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- PDB-3sc2: REFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-A... -

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Basic information

Entry
Database: PDB / ID: 3sc2
TitleREFINED ATOMIC MODEL OF WHEAT SERINE CARBOXYPEPTIDASE II AT 2.2-ANGSTROMS RESOLUTION
Components(SERINE CARBOXYPEPTIDASE II (CPDW-II)) x 2
KeywordsHYDROLASE(CARBOXYPEPTIDASE)
Function / homology
Function and homology information


carboxypeptidase D / serine-type carboxypeptidase activity / proteolysis
Similarity search - Function
Rossmann fold - #11320 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #940 / Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Rossmann fold - #11320 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #940 / Serine carboxypeptidase, serine active site / Serine carboxypeptidases, serine active site. / Peptidase S10, serine carboxypeptidase / Serine carboxypeptidases, histidine active site / Serine carboxypeptidase / Serine carboxypeptidases, histidine active site. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine carboxypeptidase 2
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsLiao, D.-I. / Remington, S.J.
Citation
Journal: Biochemistry / Year: 1992
Title: Refined atomic model of wheat serine carboxypeptidase II at 2.2-A resolution.
Authors: Liao, D.I. / Breddam, K. / Sweet, R.M. / Bullock, T. / Remington, S.J.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Structure of Wheat Serine Carboxypeptidase II at 3.5 Angstroms Resolution
Authors: Liao, D.-I. / Remington, S.J.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization of Serine Carboxypeptidases
Authors: Wilson, K.P. / Liao, D.-I. / Bullock, T. / Remington, S.J. / Breddam, K.
#3: Journal: Carlsberg Res.Commun. / Year: 1987
Title: Primary Structure and Enzymatic Properties of Carboxypeptidase II from Wheat Bran
Authors: Breddam, K. / Sorensen, S.B. / Svendsen, I.
History
DepositionJul 1, 1992Processing site: BNL
SupersessionOct 15, 1993ID: 2SC2
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.pdbx_PDB_ins_code / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.PDB_ins_code / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.PDB_ins_code_2 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
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_seq_id / _atom_site.label_asym_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id
Remark 700SHEET THE SECONDARY STRUCTURE ASSIGNMENT IS ACCORDING TO KABSCH AND SANDER (BIOPOLYMERS 22, 2577- ...SHEET THE SECONDARY STRUCTURE ASSIGNMENT IS ACCORDING TO KABSCH AND SANDER (BIOPOLYMERS 22, 2577-2637, 1983) DSSP PROGRAM EXCEPT FOR RESIDUES -1 TO 1 AND 102 TO 105. BOTH STRANDS ARE INVOLVED IN THE HYDROGEN BONDING OF A BETA SHEET, BUT NEITHER OF THEM IS ASSIGNED AS A BETA STRAND BY DSSP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE CARBOXYPEPTIDASE II (CPDW-II)
B: SERINE CARBOXYPEPTIDASE II (CPDW-II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7885
Polymers45,8982
Non-polymers1,8903
Water3,549197
1
A: SERINE CARBOXYPEPTIDASE II (CPDW-II)
B: SERINE CARBOXYPEPTIDASE II (CPDW-II)
hetero molecules

A: SERINE CARBOXYPEPTIDASE II (CPDW-II)
B: SERINE CARBOXYPEPTIDASE II (CPDW-II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,57610
Polymers91,7964
Non-polymers3,7806
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)98.400, 98.400, 209.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: THERE IS NO APPARENT ELECTRON DENSITY FOR THE SIDE CHAINS OF RESIDUES GLU A 24, LYS A 163, ARG B 282, THR B 293, AND GLN B 375A. THE SIDE CHAINS ARE MODELLED WITH ZERO OCCUPANCY.
2: RESIDUES PRO A 43, PRO A 54, AND PRO A 96 ARE CIS PROLINES.

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Components

#1: Protein SERINE CARBOXYPEPTIDASE II (CPDW-II)


Mass: 28705.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / References: UniProt: P08819, EC: 3.4.16.1
#2: Protein SERINE CARBOXYPEPTIDASE II (CPDW-II)


Mass: 17192.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P08819, EC: 3.4.16.1
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1a_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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-ManpNAc]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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

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Sample preparation

CrystalDensity Matthews: 5.52 Å3/Da / Density % sol: 77.74 %
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12-3 mg/mlprotein1drop
20.25 Msodium chloride1drop
31-4 %PEG15501drop
440 mMsodium acetate1drop
51.5 2.01reservoirMNaCl
640 mMsodium acetate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 38081 / % possible obs: 72.9 % / Num. measured all: 103780

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.169 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 126 197 3533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. reflection obs: 35941 / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.8

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