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- PDB-4iyj: Crystal structure of a putative acylhydrolase (BACUNI_03406) from... -

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Basic information

Entry
Database: PDB / ID: 4iyj
TitleCrystal structure of a putative acylhydrolase (BACUNI_03406) from Bacteroides uniformis ATCC 8492 at 1.37 A resolution
ComponentsGDSL-like protein
KeywordsHYDROLASE / PF13472 family / GDSL-like Lipase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


: / 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
Unknown ligand / GDSL-like protein
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.37 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative acylhydrolase (BACUNI_03406) from Bacteroides uniformis ATCC 8492 at 1.37 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 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
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GDSL-like protein
B: GDSL-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8017
Polymers47,6382
Non-polymers1635
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-29 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.899, 61.282, 124.514
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 GDSL-like protein


Mass: 23819.223 Da / Num. of mol.: 2 / Fragment: UNP residues 18-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Plasmid: SpeedE5T / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V743
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 18-228) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 18-228) 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.00% 2-propanol, 20.00% polyethylene glycol 4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.918401,0.979415
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2012 / 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
10.9184011
20.9794151
ReflectionResolution: 1.37→29.552 Å / Num. all: 93097 / Num. obs: 93097 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rsym value: 0.093 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.37-1.413.50.880.82369068320.8899.5
1.41-1.443.50.70212310166640.70299.8
1.44-1.493.50.5161.42253064760.51699.8
1.49-1.533.50.3961.82213563010.39699.8
1.53-1.583.50.3332.12145060750.33399.6
1.58-1.643.50.2642.72096259140.26499.5
1.64-1.73.60.2213.32034056940.22199.3
1.7-1.773.60.1754.11958654610.17599.1
1.77-1.853.60.14351882352460.14399.1
1.85-1.943.60.1195.91806350450.11999.1
1.94-2.043.60.1016.71707547840.10199.3
2.04-2.173.50.0917.41617045730.09199.5
2.17-2.323.50.0867.61523143070.08699.6
2.32-2.53.50.0837.81399440230.08399.7
2.5-2.743.40.0817.81278337230.08199.7
2.74-3.063.30.07291120933530.07298.7
3.06-3.543.30.06110.5968729630.06199.3
3.54-4.333.60.0512.9924325440.0599.4
4.33-6.133.60.04613.8719119980.04698.8
6.13-29.5523.40.04215386511210.04295.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.37→29.552 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 1.766 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052
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. CHLORIDE (CL) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION/CRYO CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE. 4.UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED INTO THE PUTATIVE ACTIVE SITE.IDENTIFICATION OF THE PUTATIVE ACTIVE SITE IS BASED ON ElECTRON DENSITY AND STRUCTURAL COMPARISONS WITH SIMILAR PROTEINS OF KNOWN FUNCTION. 5.THE SIDECHAINS OF GLU B177,ASP B193,GLU A211, AND GLU B33 SHOW ELEVATED NEGATIVE DIFFERENCE DENSITY. THE OCCUPANCIES OF THE SIDECHAIN ATOMS WERE NOT ADJUSTED IN THESE REGIONS OF APPARENT RADIATION DAMAGE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1732 4655 5 %RANDOM
Rwork0.1337 ---
obs0.1356 92858 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 57.44 Å2 / Biso mean: 18.4822 Å2 / Biso min: 3.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.37→29.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 13 694 3983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223498
X-RAY DIFFRACTIONr_bond_other_d0.0010.022398
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9564757
X-RAY DIFFRACTIONr_angle_other_deg0.92635870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.455459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76824.821168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59815629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1861521
X-RAY DIFFRACTIONr_chiral_restr0.0940.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023978
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
X-RAY DIFFRACTIONr_mcbond_it2.35432153
X-RAY DIFFRACTIONr_mcbond_other1.3373882
X-RAY DIFFRACTIONr_mcangle_it3.22453473
X-RAY DIFFRACTIONr_scbond_it4.38481345
X-RAY DIFFRACTIONr_scangle_it6.152111264
X-RAY DIFFRACTIONr_rigid_bond_restr1.76735896
X-RAY DIFFRACTIONr_sphericity_free7.3843704
X-RAY DIFFRACTIONr_sphericity_bonded3.39735813
LS refinement shellResolution: 1.37→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 333 -
Rwork0.229 6457 -
all-6790 -
obs--98.91 %

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