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- PDB-3llc: Crystal structure of Putative hydrolase (YP_002548124.1) from Agr... -

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Basic information

Entry
Database: PDB / ID: 3llc
TitleCrystal structure of Putative hydrolase (YP_002548124.1) from Agrobacterium vitis S4 at 1.80 A resolution
ComponentsPutative hydrolase
KeywordsHYDROLASE / Putative hydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


mycophenolic acid acyl-glucuronide esterase / palmitoyl[protein] hydrolase / hydrolase activity
Similarity search - Function
: / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Palmitoyl-protein thioesterase ABHD10, mitochondrial
Similarity search - Component
Biological speciesAgrobacterium vitis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative hydrolase (YP_002548124.1) from Agrobacterium vitis S4 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 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

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Assembly

Deposited unit
A: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6439
Polymers29,9971
Non-polymers6468
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.652, 112.652, 59.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative hydrolase


Mass: 29997.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium vitis (bacteria) / Strain: S4 / ATCC BAA-846 / Gene: Avi_0199 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B9JYM4

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Non-polymers , 5 types, 260 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2000M NaCl, 20.0000% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97949,0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 7, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979491
30.979341
ReflectionResolution: 1.8→28.763 Å / Num. obs: 35908 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.107 % / Biso Wilson estimate: 26.331 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.7062222206124196.5
1.86-1.940.4862.9271697263199.6
1.94-2.030.3463.9262466907199.9
2.03-2.130.2265.9242346359199.7
2.13-2.270.1618270927081199.8
2.27-2.440.11610.7250236554199.8
2.44-2.690.08713.8264636909199.6
2.69-3.070.06517.9250806585199.5
3.07-3.870.04425256656823199.1
3.87-28.7630.03230.7256266786199.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→28.763 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.795 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.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. 4.PEG3350 FRAGMENTS (PEG AND PG4) AND CHLORIDE (CL) FROM THE CRYSTALLIZATION SOLUTION AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1788 5 %RANDOM
Rwork0.16 ---
obs0.161 35855 99.54 %-
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: 90.04 Å2 / Biso mean: 27.838 Å2 / Biso min: 10.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20 Å2
2---1.48 Å20 Å2
3---2.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 41 252 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222207
X-RAY DIFFRACTIONr_bond_other_d0.0010.021542
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9813014
X-RAY DIFFRACTIONr_angle_other_deg0.95133769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0955307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77223.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9215374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8851522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_mcbond_it1.72431368
X-RAY DIFFRACTIONr_mcbond_other0.4923553
X-RAY DIFFRACTIONr_mcangle_it2.76652221
X-RAY DIFFRACTIONr_scbond_it4.2938839
X-RAY DIFFRACTIONr_scangle_it6.40111769
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 114 -
Rwork0.267 2412 -
all-2526 -
obs--96.27 %
Refinement TLS params.Method: refined / Origin x: 31.8381 Å / Origin y: 3.6172 Å / Origin z: -0.0326 Å
111213212223313233
T0.0494 Å2-0.0072 Å2-0.0054 Å2-0.0568 Å20.0018 Å2--0.0141 Å2
L2.2502 °2-0.5615 °2-0.1807 °2-2.839 °2-0.3919 °2--0.9559 °2
S0.0035 Å °-0.0247 Å °-0.1553 Å °-0.0064 Å °-0.0341 Å °-0.0437 Å °0.0686 Å °-0.0085 Å °0.0306 Å °

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