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- PDB-3epr: Crystal structure of putative HAD superfamily hydrolase from Stre... -

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Basic information

Entry
Database: PDB / ID: 3epr
TitleCrystal structure of putative HAD superfamily hydrolase from Streptococcus agalactiae.
ComponentsHydrolase, haloacid dehalogenase-like family
KeywordsHYDROLASE / structural genomics / UNKNOWN FUNCTION / HAD superfamily hydrolase. / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / hydrolase activity / metal ion binding
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIA, hypothetical 1 / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acid sugar phosphatase
Similarity search - Component
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsRamagopal, U.A. / Toro, R. / Dickey, M. / Tang, B.K. / Groshong, C. / Rodgers, L. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative HAD superfamily hydrolase from Streptococcus agalactiae.
Authors: Ramagopal, U.A. / Toro, R. / Dickey, M. / Tang, B.K. / Groshong, C. / Rodgers, L. / Burley, S.K. / Almo, S.C.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2263
Polymers29,1111
Non-polymers1152
Water5,080282
1
A: Hydrolase, haloacid dehalogenase-like family
hetero molecules

A: Hydrolase, haloacid dehalogenase-like family
hetero molecules

A: Hydrolase, haloacid dehalogenase-like family
hetero molecules

A: Hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,90512
Polymers116,4444
Non-polymers4608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10410 Å2
ΔGint-83 kcal/mol
Surface area39420 Å2
MethodPISA
2
A: Hydrolase, haloacid dehalogenase-like family
hetero molecules

A: Hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4526
Polymers58,2222
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area3110 Å2
ΔGint-36 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.367, 82.954, 99.604
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Hydrolase, haloacid dehalogenase-like family


Mass: 29111.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Gene: SAG0892 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8E044
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 25% PEG3350, 0.2 M Ammonium Acetate, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.979
SYNCHROTRONNSLS X12C20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 15, 2008
ADSC QUANTUM 42CCDAug 15, 2008
Radiation
IDProtocolScattering typeWavelength-IDMonochromatic (M) / Laue (L)
1SADx-ray1
2SADx-ray1M
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 48500 / Num. obs: 48500 / % possible obs: 97.1 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.103 / Rsym value: 0.082 / Χ2: 1.184 / Net I/σ(I): 29.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.64 / Num. unique all: 4530 / Rsym value: 0.553 / Χ2: 0.964 / % possible all: 91.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
SHELXEmodel building
SHELXDphasing
RefinementResolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.872 / SU B: 1.282 / SU ML: 0.047 / SU R Cruickshank DPI: 0.071 / SU Rfree: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2443 5.1 %RANDOM
Rwork0.179 ---
obs0.18 48286 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.96 Å2 / Biso mean: 21.473 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.6 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 7 282 2291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222051
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.982796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9395261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8525.45588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79215343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.638159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021539
X-RAY DIFFRACTIONr_nbd_refined0.2080.2979
X-RAY DIFFRACTIONr_nbtor_refined0.310.21451
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2214
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.216
X-RAY DIFFRACTIONr_mcbond_it0.9191.51295
X-RAY DIFFRACTIONr_mcangle_it1.56522102
X-RAY DIFFRACTIONr_scbond_it2.4283778
X-RAY DIFFRACTIONr_scangle_it3.8014.5693
LS refinement shellResolution: 1.548→1.588 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 191 -
Rwork0.246 3069 -
all-3260 -
obs--88.88 %

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