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- PDB-3fef: Crystal structure of putative glucosidase lplD from bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 3fef
TitleCrystal structure of putative glucosidase lplD from bacillus subtilis
ComponentsPutative glucosidase lplD, ALPHA-GALACTURONIDASE
KeywordsHYDROLASE / lplD / gulosidase / structural genomics / UNKNOWN FUNCTION / Glycosidase / Manganese / Metal-binding / NAD / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


galacturonan 1,4-alpha-galacturonidase / galacturan 1,4-alpha-galacturonidase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding / cytosol
Similarity search - Function
LDH C-terminal domain-like / AglA-like glucosidase / Glycoside hydrolase, family 4, conserved site / : / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal ...LDH C-terminal domain-like / AglA-like glucosidase / Glycoside hydrolase, family 4, conserved site / : / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Alpha-galacturonidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsRamagopal, U.A. / Rajashankar, K.R. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Crystal structure of putative glucosidase lplD from bacillus subtilis.
Authors: Ramagopal, U.A. / Rajashankar, K.R. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionNov 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2013Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative glucosidase lplD, ALPHA-GALACTURONIDASE
B: Putative glucosidase lplD, ALPHA-GALACTURONIDASE
C: Putative glucosidase lplD, ALPHA-GALACTURONIDASE
D: Putative glucosidase lplD, ALPHA-GALACTURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,86915
Polymers202,0994
Non-polymers77011
Water9,638535
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-162 kcal/mol
Surface area62390 Å2
MethodPISA
2
A: Putative glucosidase lplD, ALPHA-GALACTURONIDASE
C: Putative glucosidase lplD, ALPHA-GALACTURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3867
Polymers101,0502
Non-polymers3375
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-63 kcal/mol
Surface area33490 Å2
MethodPISA
3
B: Putative glucosidase lplD, ALPHA-GALACTURONIDASE
D: Putative glucosidase lplD, ALPHA-GALACTURONIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4838
Polymers101,0502
Non-polymers4336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-82 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.987, 84.843, 86.051
Angle α, β, γ (deg.)69.800, 68.100, 64.070
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 7 - 440 / Label seq-ID: 3 - 436

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
Detailsunknown

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Components

#1: Protein
Putative glucosidase lplD, ALPHA-GALACTURONIDASE


Mass: 50524.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU07130, lplD / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P39130, galacturonan 1,4-alpha-galacturonidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 23% PEG 3350, 0.17M Ammonium Sulphate, 0.1M Magnesium Acetate, pH 7.0, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 90052 / Num. obs: 90052 / % possible obs: 94 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Rsym value: 0.068 / Χ2: 1.171 / Net I/σ(I): 10.697
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 5.1 / Num. unique all: 6125 / Rsym value: 0.175 / Χ2: 0.737 / % possible all: 63.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.265 / WRfactor Rwork: 0.2 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.85 / SU B: 5.156 / SU ML: 0.136 / SU R Cruickshank DPI: 0.297 / SU Rfree: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 4505 5 %RANDOM
Rwork0.187 ---
obs0.19 90052 93.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.23 Å2 / Biso mean: 33.364 Å2 / Biso min: 12.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å21.17 Å21.02 Å2
2---0.73 Å20.64 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13534 0 39 535 14108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213848
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.95818784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52951734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09523.815650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.951152323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.40715111
X-RAY DIFFRACTIONr_chiral_restr0.080.22089
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110571
X-RAY DIFFRACTIONr_mcbond_it1.82528614
X-RAY DIFFRACTIONr_mcangle_it2.819313858
X-RAY DIFFRACTIONr_scbond_it2.64925234
X-RAY DIFFRACTIONr_scangle_it3.80434926
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1732MEDIUM POSITIONAL0.170.5
B1732MEDIUM POSITIONAL0.130.5
C1732MEDIUM POSITIONAL0.190.5
D1732MEDIUM POSITIONAL0.140.5
A1638LOOSE POSITIONAL0.35
B1638LOOSE POSITIONAL0.35
C1638LOOSE POSITIONAL0.345
D1638LOOSE POSITIONAL0.365
A1732MEDIUM THERMAL1.452
B1732MEDIUM THERMAL22
C1732MEDIUM THERMAL2.222
D1732MEDIUM THERMAL1.952
A1638LOOSE THERMAL1.5310
B1638LOOSE THERMAL1.9210
C1638LOOSE THERMAL2.0910
D1638LOOSE THERMAL1.810
LS refinement shellResolution: 2.197→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 174 -
Rwork0.178 3929 -
all-4103 -
obs--57.62 %

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