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- PDB-2zyi: A. Fulgidus lipase with fatty acid fragment and calcium -

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Basic information

Entry
Database: PDB / ID: 2zyi
TitleA. Fulgidus lipase with fatty acid fragment and calcium
ComponentsLipase, putative
KeywordsHYDROLASE / lipase / Archaeoglobus fulgidus / fatty acid
Function / homology
Function and homology information


acyltransferase activity / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2190 / Immunoglobulin-like - #2200 / AFL, C-terminal / : / Lipase C-terminal domain / AF_1763-like, C-terminal domain / Alpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain ...Immunoglobulin-like - #2190 / Immunoglobulin-like - #2200 / AFL, C-terminal / : / Lipase C-terminal domain / AF_1763-like, C-terminal domain / Alpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
STEARIC ACID / Lipase, putative
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, C.K. / Ko, T.P. / Guo, R.T. / Wang, A.H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure of the alkalohyperthermophilic Archaeoglobus fulgidus lipase contains a unique C-terminal domain essential for long-chain substrate binding.
Authors: Chen, C.K. / Lee, G.C. / Ko, T.P. / Guo, R.T. / Huang, L.M. / Liu, H.J. / Ho, Y.F. / Shaw, J.F. / Wang, A.H.
History
DepositionJan 22, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: Lipase, putative
B: Lipase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6106
Polymers105,9612
Non-polymers6494
Water14,088782
1
A: Lipase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3053
Polymers52,9801
Non-polymers3252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3053
Polymers52,9801
Non-polymers3252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.445, 105.375, 117.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipase, putative


Mass: 52980.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_1763 / Plasmid: pET-23a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O28511, triacylglycerol lipase
#2: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M CaCl2, 0.1M Sodium acetate (pH 4.6), 10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 49774 / Num. obs: 50018 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 37
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 8.1 / Num. unique all: 4866 / % possible all: 97.6

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZYH

2zyh


Resolution: 2.3→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2430 -RANDOM
Rwork0.182 ---
all-49774 --
obs-47885 96.2 %-
Displacement parametersBiso mean: 29.53 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7126 0 40 782 7948
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.8
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.27 220 -
Rwork0.221 --
obs-4537 92.3 %

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