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- PDB-4m8k: Crystal structure of a putative GDSL-like lipase (BACUNI_00748) f... -

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Basic information

Entry
Database: PDB / ID: 4m8k
TitleCrystal structure of a putative GDSL-like lipase (BACUNI_00748) from Bacteroides uniformis ATCC 8492 at 1.90 A resolution
Componentshypothetical protein, GDSL-like Lipase/Acylhydrolase family proteinHypothesis
KeywordsHYDROLASE / GDSL-like Lipase/Acylhydrolase family / PF13472 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyPutative GDSL-like Lipase/Acylhydrolase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACUNI_00748) from Bacteroides uniformis ATCC 8492 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
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

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Assembly

Deposited unit
A: hypothetical protein, GDSL-like Lipase/Acylhydrolase family protein
B: hypothetical protein, GDSL-like Lipase/Acylhydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4157
Polymers54,1672
Non-polymers2485
Water5,711317
1
A: hypothetical protein, GDSL-like Lipase/Acylhydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1783
Polymers27,0841
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein, GDSL-like Lipase/Acylhydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2374
Polymers27,0841
Non-polymers1543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-33 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.244, 72.319, 62.900
Angle α, β, γ (deg.)90.000, 91.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein, GDSL-like Lipase/Acylhydrolase family protein / Hypothesis


Mass: 27083.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: BACUNI_00748, ZP_02069338.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7UZL6
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 23-239) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED ...THIS CONSTRUCT (RESIDUES 23-239) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M ammonium acetate, 30.0% polyethylene glycol 4000, 0.1M sodium citrate pH 5.6, 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: 0.97971,0.91837,0.97908
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979711
20.918371
30.979081
ReflectionResolution: 1.9→29.142 Å / Num. obs: 34218 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.196 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.973.40.6431.3311355644190.8
1.97-2.050.412211951656595.6
2.05-2.140.3252.711449634495.5
2.14-2.250.2683.211149631694.7
2.25-2.390.2173.911084638793.8
2.39-2.580.1575.212417680896.3
2.58-2.840.1137.311820655796
2.84-3.250.06211.311502651495.5
3.25-4.080.03420.111850649696.2
4.08-29.140.02624.711773659194.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.142 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 6.631 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.137
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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. 3.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.ACETATE (ACT) FROM THE CRYSTALLIZATION SOLUTION AND CHLORIDE (CL) FROM THE PURIFICATION BUFFERS HAVE BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 1717 5 %RANDOM
Rwork0.1601 ---
obs0.1625 34197 97.96 %-
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 max: 105.62 Å2 / Biso mean: 28.1579 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å2-0 Å2-0.75 Å2
2---2.69 Å2-0 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 14 317 3756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193581
X-RAY DIFFRACTIONr_bond_other_d0.0050.023153
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9234881
X-RAY DIFFRACTIONr_angle_other_deg1.01637272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0845439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42424.162185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63715540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4261516
X-RAY DIFFRACTIONr_chiral_restr0.0640.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024161
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02903
X-RAY DIFFRACTIONr_mcbond_it3.1463.5281717
X-RAY DIFFRACTIONr_mcbond_other3.0973.5181713
X-RAY DIFFRACTIONr_mcangle_it3.7476.5622143
LS refinement shellResolution: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 113 -
Rwork0.284 2314 -
all-2427 -
obs--93.92 %
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)
10.9752-0.03440.16830.5621-0.10210.7050.00870.0790.0057-0.06420.00290.03360.0290.0053-0.01160.0395-0.00040.01110.06280.0120.046129.10711.197532.9427
20.6625-0.15070.00181.15410.05050.954-0.0214-0.0485-0.00560.130.009-0.0504-0.00350.02520.01240.04810.0070.00910.07390.00380.063347.6281-9.227857.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 228
2X-RAY DIFFRACTION2B-5 - 228

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