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- PDB-1z8h: CRYSTAL STRUCTURE OF a GDSL-like lipase (ALR1529) FROM NOSTOC SP.... -

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Basic information

Entry
Database: PDB / ID: 1z8h
TitleCRYSTAL STRUCTURE OF a GDSL-like lipase (ALR1529) FROM NOSTOC SP. PCC 7120 AT 2.02 A RESOLUTION
ComponentsPutative lipase from the G-D-S-L family
KeywordsHYDROLASE / PUTATIVE LIPASE FROM THE G-D-S-L FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


lysophospholipase activity
Similarity search - Function
: / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Unknown ligand / Alr1529 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.02 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative lipase from the G-D-S-L family (17135349) from Nostoc sp. PCC 7120 at 2.02 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: Putative lipase from the G-D-S-L family
B: Putative lipase from the G-D-S-L family
C: Putative lipase from the G-D-S-L family
D: Putative lipase from the G-D-S-L family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,08911
Polymers100,9094
Non-polymers1807
Water14,754819
1
A: Putative lipase from the G-D-S-L family
B: Putative lipase from the G-D-S-L family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5756
Polymers50,4542
Non-polymers1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint12 kcal/mol
Surface area16940 Å2
MethodPISA
2
C: Putative lipase from the G-D-S-L family
D: Putative lipase from the G-D-S-L family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5145
Polymers50,4542
Non-polymers603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint7 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.504, 69.806, 211.028
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
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End label comp-ID: LEU / Refine code: 6

Dom-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSAA6 - 20218 - 214
2THRBB7 - 20219 - 214
3LYSCC6 - 20218 - 214
4LYSDD6 - 20218 - 214

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Components

#1: Protein
Putative lipase from the G-D-S-L family


Mass: 25227.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr1529 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YWS4
#2: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / 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: 2.3 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 10% NP_Isopropanol, 0.06M HEPES, 0.04M HEPES_Na, 12% PEG 4000, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9787, 1.0332,0.9784
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 31, 2003 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
21.03321
30.97841
ReflectionResolution: 2.02→49.55 Å / Num. obs: 62663 / % possible obs: 98.95 % / Redundancy: 9.6 % / Biso Wilson estimate: 31.55 Å2 / Rsym value: 0.074 / Net I/σ(I): 26.76
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 7.85 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 5908 / Rsym value: 0.348 / % possible all: 95.27

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
autoSHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 2.02→49.55 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.978 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.142
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THIS PROTEIN CONSISTS OF A CONSERVED SER-HIS-ASP (17-182-179) TRIAD. AN UNKNOWN INTERMEDIATE WAS OBSERVED ON SER 17. WILD TYPE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THIS PROTEIN CONSISTS OF A CONSERVED SER-HIS-ASP (17-182-179) TRIAD. AN UNKNOWN INTERMEDIATE WAS OBSERVED ON SER 17. WILD TYPE STRUCTURE FOR THIS PROTEIN IS ALSO DEPOSITED AS PDB ENTRY 1VJG.
RfactorNum. reflection% reflectionSelection details
Rfree0.19469 3162 5.1 %RANDOM
Rwork0.15466 ---
obs0.1567 59429 98.79 %-
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: 22.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--2.08 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.02→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6401 0 36 819 7256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226712
X-RAY DIFFRACTIONr_bond_other_d0.0010.026020
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9539166
X-RAY DIFFRACTIONr_angle_other_deg0.867313975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.095814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85624.072334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.678151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5181551
X-RAY DIFFRACTIONr_chiral_restr0.0860.21015
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027464
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021383
X-RAY DIFFRACTIONr_nbd_refined0.2190.21523
X-RAY DIFFRACTIONr_nbd_other0.1940.26381
X-RAY DIFFRACTIONr_nbtor_other0.0840.23836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2705
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.225
X-RAY DIFFRACTIONr_mcbond_it1.0471.54124
X-RAY DIFFRACTIONr_mcbond_other0.2341.51633
X-RAY DIFFRACTIONr_mcangle_it1.41926578
X-RAY DIFFRACTIONr_scbond_it2.27732984
X-RAY DIFFRACTIONr_scangle_it3.3094.52581
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23334
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1940.22
Refine LS restraints NCS

Ens-ID: 1 / Number: 2810 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.545
2Bloose positional0.545
3Cloose positional0.645
4Dloose positional0.615
1Aloose thermal3.9510
2Bloose thermal2.9110
3Cloose thermal2.9210
4Dloose thermal3.0310
LS refinement shellResolution: 2.02→2.074 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 198 4.63 %
Rwork0.174 4082 -
obs--92.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1411-0.0695-0.18550.7273-0.05211.14710.0654-0.04730.0301-0.00860.00840.0213-0.1138-0.0191-0.0738-0.0745-0.00460.0205-0.0415-0.0181-0.069549.877322.8515202.7828
21.243-0.0615-0.63791.4767-0.24151.980.1689-0.02730.255-0.027-0.0135-0.0628-0.51230.191-0.15540.0661-0.06430.0725-0.0831-0.016-0.027362.124140.1234185.2614
30.8189-0.1505-0.07861.09620.41771.4048-0.02610.0078-0.0242-0.0009-0.0019-0.09510.13230.16070.0281-0.0385-0.01290.02-0.0663-0.0158-0.033767.20833.8616168.522
41.806-0.0071-0.53591.23640.06151.0259-0.13140.345-0.0477-0.13680.09220.12860.0857-0.33790.0392-0.0644-0.0938-0.030.0433-0.0293-0.068139.72016.8931167.2047
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 20617 - 218
22BB7 - 20519 - 217
33CC6 - 20518 - 217
44DD6 - 20618 - 218

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