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- PDB-1tcb: THE SEQUENCE, CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT OF T... -

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Basic information

Entry
Database: PDB / ID: 1tcb
TitleTHE SEQUENCE, CRYSTAL STRUCTURE DETERMINATION AND REFINEMENT OF TWO CRYSTAL FORMS OF LIPASE B FROM CANDIDA ANTARCTICA
ComponentsLIPASE
KeywordsHYDROLASE(CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
: / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCandida antarctica (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsUppenberg, J. / Jones, T.A.
Citation
Journal: Structure / Year: 1994
Title: The sequence, crystal structure determination and refinement of two crystal forms of lipase B from Candida antarctica.
Authors: Uppenberg, J. / Hansen, M.T. / Patkar, S. / Jones, T.A.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Studies of Lipase B from Candida Antarctica
Authors: Uppenberg, J. / Patkar, S. / Bergfors, T. / Jones, T.A.
History
DepositionFeb 28, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: 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: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / 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 / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: LIPASE
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0905
Polymers66,0802
Non-polymers1,0093
Water8,467470
1
A: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7573
Polymers33,0401
Non-polymers7172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3332
Polymers33,0401
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.200, 50.500, 86.700
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 70 / 2: CIS PROLINE - PRO A 192 / 3: CIS PROLINE - PRO B 70 / 4: CIS PROLINE - PRO B 192
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2738, 0.9363, 0.2201), (0.9383, -0.3102, 0.1525), (0.2111, 0.1647, -0.9635)
Vector: -4.0635, -1.0129, 27.2489)
DetailsTHIS IS THE LOW PH STRUCTURE OF THE MONOCLINIC CRYSTAL; FORM WITH TWO MOLECULES IN THE ASYMMETRIC UNIT. THE MOLECULES ARE CALLED A AND B. THE RMS DEVIATIONS ARE 0.18 ANGSTROMS FOR C-ALPHAS AND 0.31 ANGSTROMS FOR ALL ATOMS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A.

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Components

#1: Protein LIPASE


Mass: 33040.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida antarctica (fungus) / References: UniProt: P41365, triacylglycerol lipase
#2: 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
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE DNA SEQUENCE OF J.UPPENBERG ET AL., ...THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE DNA SEQUENCE OF J.UPPENBERG ET AL., 1994, LISTED IN THE JRNL REFERENCE ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal grow
*PLUS
pH: 3.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG40001reservoir
250 mMsodium acetate1reservoir
310 %isopropanol1reservoir
410 mg/mlprotein1drop
50.6 %beta-octyl glucoside1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 31323 / % possible obs: 86 % / Num. measured all: 58582 / Rmerge(I) obs: 0.03

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→7.5 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.187 -
obs0.187 31323
Refinement stepCycle: LAST / Resolution: 2.1→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 68 470 5186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg0.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.187 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 0.9

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