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- PDB-2hih: Crystal structure of Staphylococcus hyicus lipase -

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Basic information

Entry
Database: PDB / ID: 2hih
TitleCrystal structure of Staphylococcus hyicus lipase
ComponentsLipase 46 kDa form
KeywordsHYDROLASE / lipase / A1 phospholipase / phospholipid binding
Function / homology
Function and homology information


phospholipase A1 / glycerophospholipase activity / glycerophospholipid phospholipase A1 activity / triglyceride catabolic process / triacylglycerol lipase / triacylglycerol lipase activity / phosphatidylcholine catabolic process / lipid catabolic process / calcium ion binding / extracellular region
Similarity search - Function
: / Lipase-like, C-terminal domain / Lipases, serine active site. / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus hyicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsTiesinga, J.J.W. / van Pouderoyen, G. / Nardini, M. / Dijkstra, B.W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis of phospholipase activity of Staphylococcus hyicus lipase.
Authors: Tiesinga, J.J. / van Pouderoyen, G. / Nardini, M. / Ransac, S. / Dijkstra, B.W.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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 46 kDa form
B: Lipase 46 kDa form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9266
Polymers96,7152
Non-polymers2114
Water46826
1
A: Lipase 46 kDa form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4633
Polymers48,3581
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase 46 kDa form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4633
Polymers48,3581
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-56 kcal/mol
Surface area32170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.310, 77.960, 169.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEALAALAAA29 - 3564 - 70
21PHEPHEALAALABB29 - 3564 - 70
32ALAALAPROPROAA7 - 1142 - 46
42ALAALAPROPROBB7 - 1142 - 46
53TYRTYRGLYGLYAA40 - 8475 - 119
63TYRTYRGLYGLYBB40 - 8475 - 119
74GLNGLNLYSLYSAA201 - 221236 - 256
84GLNGLNLYSLYSBB201 - 221236 - 256
95GLYGLYSERSERAA283 - 326318 - 361
105GLYGLYSERSERBB283 - 326318 - 361
116LYSLYSSERSERAA329 - 337364 - 372
126LYSLYSSERSERBB329 - 337364 - 372
137HISHISSERSERAA368 - 392403 - 427
147HISHISSERSERBB368 - 392403 - 427
158PROPROGLYGLYAA14 - 2549 - 60
168PROPROGLYGLYBB14 - 2549 - 60
179VALVALSERSERAA86 - 198121 - 233
189VALVALSERSERBB86 - 198121 - 233
1910GLYGLYASNASNAA223 - 258258 - 293
2010GLYGLYASNASNBB223 - 258258 - 293
2111LEULEUTHRTHRAA339 - 366374 - 401
2211LEULEUTHRTHRBB339 - 366374 - 401
2312LYSLYSHISHISAA260 - 278295 - 313
2412LYSLYSHISHISBB260 - 278295 - 313

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Components

#1: Protein Lipase 46 kDa form


Mass: 48357.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus hyicus (bacteria) / Gene: lip / Plasmid: pSHT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE 3) / References: UniProt: P04635, triacylglycerol lipase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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.: 26 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NaCl, Na succinate, DMSO, isopropanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 30, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.86→26.71 Å / Num. all: 22929 / Num. obs: 22929 / % possible obs: 99 % / Redundancy: 6.1 % / Rsym value: 0.088
Reflection shellResolution: 2.86→2.93 Å / Num. unique all: 1663 / % possible all: 99.7

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Phasing

Phasing MRR rigid body: 0.488 / Cor.coef. Fo:Fc: 0.387 / Cor.coef. Io to Ic: 0.393

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Processing

Software
NameVersionClassificationNB
AMoREphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JI3

1ji3


Resolution: 2.86→26.71 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.846 / SU B: 13.948 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2322 10.1 %RANDOM
Rwork0.208 ---
all0.213 22929 --
obs0.213 22929 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.86→26.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6143 0 4 26 6173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0216302
X-RAY DIFFRACTIONr_bond_other_d0.0010.025348
X-RAY DIFFRACTIONr_angle_refined_deg0.7861.9258526
X-RAY DIFFRACTIONr_angle_other_deg0.584312512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7835771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14624.5320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.114151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1571526
X-RAY DIFFRACTIONr_chiral_restr0.0490.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027143
X-RAY DIFFRACTIONr_gen_planes_other00.021305
X-RAY DIFFRACTIONr_nbd_refined0.2020.31368
X-RAY DIFFRACTIONr_nbd_other0.1920.35376
X-RAY DIFFRACTIONr_nbtor_refined0.190.53027
X-RAY DIFFRACTIONr_nbtor_other0.0880.53573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.5279
X-RAY DIFFRACTIONr_metal_ion_refined0.130.510
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.324
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.58
X-RAY DIFFRACTIONr_mcbond_it0.1641.53912
X-RAY DIFFRACTIONr_mcbond_other0.031.51606
X-RAY DIFFRACTIONr_mcangle_it0.28626103
X-RAY DIFFRACTIONr_scbond_it0.35532756
X-RAY DIFFRACTIONr_scangle_it0.5824.52423
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5415 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.180.5
MEDIUM THERMAL0.142
LS refinement shellResolution: 2.86→2.934 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 165 -
Rwork0.275 1498 -
obs-1663 100 %

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