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- PDB-1mkv: CARBOXYLIC ESTER HYDROLASE COMPLEX (PLA2 + TRANSITION STATE ANALO... -

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Basic information

Entry
Database: PDB / ID: 1mkv
TitleCARBOXYLIC ESTER HYDROLASE COMPLEX (PLA2 + TRANSITION STATE ANALOG COMPLEX)
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / ENZYME / CARBOXYLIC ESTER HYDROLASE
Function / homology
Function and homology information


Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / innate immune response in mucosa / phospholipid binding / fatty acid biosynthetic process / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of fibroblast proliferation / antibacterial humoral response / defense response to Gram-positive bacterium / signaling receptor binding / calcium ion binding / cell surface / extracellular space
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-GEL / Phospholipase A2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / THE HIGH RESOLUTION ATOMIC COORDINATES OF THE WILD TYPE / Resolution: 1.89 Å
AuthorsSundaralingam, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of the complex of bovine pancreatic phospholipase A2 with a transition-state analogue.
Authors: Sekar, K. / Kumar, A. / Liu, X. / Tsai, M.D. / Gelb, M.H. / Sundaralingam, M.
#1: Journal: To be Published
Title: 1.72 Angstrom Resolution Refinement of the Trigonal Form of Bovine Pancreatic Phospholipase A2
Authors: Sekar, K. / Sekharudu, C. / Tsai, M.-D. / Sundaralingam, M.
#2: Journal: Biochemistry / Year: 1997
Title: Crystal Structure of the Complex of Bovine Pancreatic Phospholipase A2 with the Inhibitor 1-Hexadecyl-3-(Trifluoroethyl)-Sn-Glycero-2-Phosphomethanol
Authors: Sekar, K. / Eswaramoorthy, S. / Jain, M.K. / Sundaralingam, M.
#3: Journal: Biochemistry / Year: 1997
Title: Phospholipase A2 Engineering. Structural and Functional Roles of the Highly Conserved Active Site Residue Aspartate-99
Authors: Sekar, K. / Yu, B.Z. / Rogers, J. / Lutton, J. / Liu, X. / Chen, X. / Tsai, M.D. / Jain, M.K. / Sundaralingam, M.
#4: Journal: Biochemistry / Year: 1996
Title: Phospholipase A2 Engineering. Deletion of the C-Terminus Segment Changes Substrate Specificity and Uncouples Calcium and Substrate Binding at the Zwitterionic Interface
Authors: Huang, B. / Yu, B.Z. / Rogers, J. / Byeon, I.J. / Sekar, K. / Chen, X. / Sundaralingam, M. / Tsai, M.D. / Jain, M.K.
#5: Journal: Biochemistry / Year: 1991
Title: Phospholipase A2 Engineering. X-Ray Structural and Functional Evidence for the Interaction of Lysine-56 with Substrates
Authors: Noel, J.P. / Bingman, C.A. / Deng, T.L. / Dupureur, C.M. / Hamilton, K.J. / Jiang, R.T. / Kwak, J.G. / Sekharudu, C. / Sundaralingam, M. / Tsai, M.D.
History
DepositionSep 13, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Apr 3, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3403
Polymers13,8111
Non-polymers5302
Water1,58588
1
A: PHOSPHOLIPASE A2
hetero molecules

A: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6806
Polymers27,6212
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+5/31
Unit cell
Length a, b, c (Å)46.580, 46.580, 102.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13810.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line: BL21 / Gene: MATURE PLA2 / Organ: PANCREAS / Plasmid: PTO-A2MBL21 / Gene (production host): MATURE PLA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P00593, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GEL / 1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 489.521 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H45NO8P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (20MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS ...Details: CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (20MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2.5 (MICRO)L OF 75% MPD AND 2.0 (MICRO)L OF (2MM) IN THE DROPLET. THE RESERVOIR CONTAINED (50%) OF MPD., pH 7.5, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
250 mMTris-HCl1drop
375 %MPD1drop
42 mMinhibitor1drop
550 %MPD1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Date: Nov 8, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→15 Å / Num. obs: 8758 / % possible obs: 8 % / Redundancy: 5 % / Rsym value: 0.071
Reflection shellResolution: 1.89→2.01 Å / Rsym value: 0.434
Reflection
*PLUS
% possible obs: 72 % / Num. measured all: 44425 / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: THE HIGH RESOLUTION ATOMIC COORDINATES OF THE WILD TYPE
Starting model: WILD TYPE

Resolution: 1.89→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.18 --
obs0.18 8758 72 %
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.89→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 32 88 1077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.87
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d3.6
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
LS refinement shellResolution: 1.89→1.97 Å / Total num. of bins used: 8 /
Rfactor% reflection
Rwork0.272 -
obs-51 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2OSUTSA.PAROSUTSA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 7726 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg3.6

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