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- PDB-3g8y: CRYSTAL STRUCTURE OF A PUTATIVE HYDROLASE (BVU_4111) FROM BACTERO... -

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Basic information

Entry
Database: PDB / ID: 3g8y
TitleCRYSTAL STRUCTURE OF A PUTATIVE HYDROLASE (BVU_4111) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.90 A RESOLUTION
ComponentsSusD/RagB-associated esterase-like protein
KeywordsHYDROLASE / SUSD/RAGB-ASSOCIATED ESTERASE-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyAbhydrolase, bacterial / Abhydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Abhydrolase family protein
Function and homology information
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SusD/RagB-associated esterase-like protein (YP_001301335.1) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 27, 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: SusD/RagB-associated esterase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,09814
Polymers45,2471
Non-polymers85113
Water8,485471
1
A: SusD/RagB-associated esterase-like protein
hetero molecules

A: SusD/RagB-associated esterase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,19628
Polymers90,4942
Non-polymers1,70226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area6450 Å2
ΔGint-30.7 kcal/mol
Surface area30320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.903, 75.903, 323.386
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsTHE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein SusD/RagB-associated esterase-like protein


Mass: 45246.867 Da / Num. of mol.: 1 / Fragment: UNP residues 25-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Strain: DSM 1447 / NCTC 11154 / Gene: YP_001301335.1, BVU_4111 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L7P9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE 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. THE CLONED CONSTRUCT CONTAINS RESIDUES 25-414 OF THE FULL LENGTH PROTEIN.

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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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 20.0% PEG 6000, 0.1M Bicine pH 9.0, 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, 0.97982, 0.97966
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 7, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979821
30.979661
ReflectionResolution: 1.9→29.399 Å / Num. obs: 44914 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 18.609 Å2 / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/σ(I): 4.824
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.957.20.77812324632070.778100
1.95-27.20.6811.12281331600.681100
2-2.067.30.5661.32230730710.566100
2.06-2.127.20.4591.62158529910.459100
2.12-2.197.30.37722099228940.377100
2.19-2.277.20.3281.72031528170.328100
2.27-2.367.20.2872.61976827320.287100
2.36-2.457.20.243.11906826400.24100
2.45-2.567.20.2073.61805825090.207100
2.56-2.697.20.1794.21747724320.179100
2.69-2.837.20.15251661423150.152100
2.83-37.10.12361571722100.123100
3-3.217.10.1027.21475820770.102100
3.21-3.477.10.0798.81388319680.079100
3.47-3.870.06111.11271518070.061100
3.8-4.256.90.05611.51145016480.056100
4.25-4.916.80.05511.91009814750.055100
4.91-6.016.70.0610.5854812830.06100
6.01-8.56.40.06110.5667110410.061100
8.5-29.3995.50.05310.834876370.05397.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.399 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.81 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.12
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. PEG MOLECULES FROM CRYSTALLIZATION AND ETHYLENE GLYCOL FROM CRYOPROTECTION ARE MODELED IN THIS STRUCTURE. 4. UNKNOWN ELECTRON DENSITY IS OBSERVED AND UNMODELED NEAR SER 256 AND HIS 398.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2257 5 %RANDOM
Rwork0.168 ---
obs0.17 44778 100 %-
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: 92.9 Å2 / Biso mean: 25.717 Å2 / Biso min: 9.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 55 471 3632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223330
X-RAY DIFFRACTIONr_bond_other_d0.0020.022296
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9634511
X-RAY DIFFRACTIONr_angle_other_deg1.02535583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0045410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.75123.946147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59415537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9541517
X-RAY DIFFRACTIONr_chiral_restr0.0820.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023711
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02685
X-RAY DIFFRACTIONr_nbd_refined0.210.3711
X-RAY DIFFRACTIONr_nbd_other0.1780.32376
X-RAY DIFFRACTIONr_nbtor_refined0.1870.51644
X-RAY DIFFRACTIONr_nbtor_other0.0880.51531
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5581
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2050.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.371
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.552
X-RAY DIFFRACTIONr_mcbond_it1.86132173
X-RAY DIFFRACTIONr_mcbond_other0.4533804
X-RAY DIFFRACTIONr_mcangle_it2.60253273
X-RAY DIFFRACTIONr_scbond_it4.00281481
X-RAY DIFFRACTIONr_scangle_it4.814111238
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 170 -
Rwork0.226 3023 -
all-3193 -
obs--100 %

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