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- PDB-3p94: Crystal structure of a GDSL-like Lipase (BDI_0976) from Parabacte... -

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Basic information

Entry
Database: PDB / ID: 3p94
TitleCrystal structure of a GDSL-like Lipase (BDI_0976) from Parabacteroides distasonis ATCC 8503 at 1.93 A resolution
ComponentsGDSL-like Lipase
KeywordsHYDROLASE / SERINE HYDROLASE / CATALYTIC TRIAD / GDSL-LIKE LIPASE / FLAVODOXIN-LIKE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologySGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / SGNH_hydro domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a GDSL-like Lipase (BDI_0976) from Parabacteroides distasonis ATCC 8503 at 1.93 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 1, 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_leaving_atom_flag / _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: GDSL-like Lipase
B: GDSL-like Lipase
C: GDSL-like Lipase
D: GDSL-like Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9196
Polymers92,5304
Non-polymers3882
Water12,863714
1
A: GDSL-like Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3272
Polymers23,1331
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GDSL-like Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3272
Polymers23,1331
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GDSL-like Lipase


Theoretical massNumber of molelcules
Total (without water)23,1331
Polymers23,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GDSL-like Lipase


Theoretical massNumber of molelcules
Total (without water)23,1331
Polymers23,1331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: GDSL-like Lipase
D: GDSL-like Lipase
hetero molecules

B: GDSL-like Lipase
C: GDSL-like Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9196
Polymers92,5304
Non-polymers3882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area7090 Å2
ΔGint-20 kcal/mol
Surface area32130 Å2
MethodPISA
6
A: GDSL-like Lipase
D: GDSL-like Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4593
Polymers46,2652
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-5 kcal/mol
Surface area17470 Å2
MethodPISA
7
B: GDSL-like Lipase
C: GDSL-like Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4593
Polymers46,2652
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-6 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 58.360, 98.610
Angle α, β, γ (deg.)90.000, 98.120, 90.000
Int Tables number4
Space group name H-MP1211
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A PREDOMINANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
GDSL-like Lipase


Mass: 23132.578 Da / Num. of mol.: 4 / Fragment: sequence database residues 25-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_0976 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LAN0
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 714 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 25-227) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 25-227) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / pH: 8.86
Details: 30.40% polyethylene glycol 4000, 0.20M sodium acetate, 0.1M TRIS pH 8.86, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979131
ReflectionResolution: 1.93→48.812 Å / Num. obs: 60928 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.66 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.17
Reflection shellResolution: 1.93→2 Å / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.4 / % possible all: 86.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.93→48.81 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.909 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. POLYETHYLENE GLYCOL FRAGMENT (PG4) MODELED IS PRESENT PROTEIN/CRYSTALLIZATION/CRYO BUFFER. 3. NON- CRYSTALLOGRAPHIC RESTRAINTS WERE APPLIED DURING REFINEMENT (AUTONCS). 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3086 5.07 %RANDOM
Rwork0.183 ---
obs0.184 60913 --
Displacement parametersBiso mean: 22.89 Å2
Baniso -1Baniso -2Baniso -3
1--4.1545 Å20 Å2-0.3231 Å2
2--0.876 Å20 Å2
3---3.2785 Å2
Refinement stepCycle: LAST / Resolution: 1.93→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6364 0 23 714 7101
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096707HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.969130HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3138SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes177HARMONIC2
X-RAY DIFFRACTIONt_gen_planes987HARMONIC5
X-RAY DIFFRACTIONt_it6707HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion872SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8443SEMIHARMONIC4
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2374 201 5.28 %
Rwork0.1984 3606 -
all0.2004 3807 -
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)
10.90330.0489-0.1420.91790.20130.8716-0.03720.025-0.0896-0.04180.02430.02320.0295-0.02030.0128-0.1013-0.00680.0245-0.03770.00220.000813.891119.701511.9436
21.0145-0.0119-0.08760.58340.12030.7586-0.0221-0.08480.07560.00260.0266-0.0564-0.03410.0425-0.0045-0.08080.00140.0109-0.0423-0.02070.0013-23.918637.444932.5281
30.52680.203-0.00240.77370.50510.89230.04470.0107-0.0405-0.00120.0356-0.09110.05520.0691-0.0803-0.07510.00890.0238-0.0553-0.01140.0192-25.856214.384411.6764
40.8738-0.03570.0571.14940.49891.21330.0323-0.15980.05890.0725-0.01570.0293-0.00220.0057-0.0166-0.11390.02390.0267-0.0055-0.0053-0.041115.494637.122837.6645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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