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- PDB-3hfq: Crystal structure of the lp_2219 protein from Lactobacillus plant... -

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Basic information

Entry
Database: PDB / ID: 3hfq
TitleCrystal structure of the lp_2219 protein from Lactobacillus plantarum. Northeast Structural Genomics Consortium Target LpR118.
Componentsuncharacterized protein lp_2219
Keywordsstructural genomics / unknown function / Q88V64_LACPL / Lp_2219 / NESG / LpR118 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


6-phosphogluconolactonase / 6-phosphogluconolactonase activity / cytosol
Similarity search - Function
: / Lactonase, 7-bladed beta propeller / Lactonase, 7-bladed beta-propeller / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / 6-phosphogluconolactonase / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.963 Å
AuthorsVorobiev, S.M. / Scott, L. / Schauder, C. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S.M. / Scott, L. / Schauder, C. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the lp_2219 protein from Lactobacillus plantarum.
Authors: Vorobiev, S.M. / Scott, L. / Schauder, C. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Maglaqui, M. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMay 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 13, 2021Group: 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 1.4Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein lp_2219
B: uncharacterized protein lp_2219
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8194
Polymers75,6292
Non-polymers1902
Water7,134396
1
A: uncharacterized protein lp_2219
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9092
Polymers37,8141
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein lp_2219
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9092
Polymers37,8141
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.543, 54.029, 79.584
Angle α, β, γ (deg.)90.000, 104.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein uncharacterized protein lp_2219


Mass: 37814.328 Da / Num. of mol.: 2 / Mutation: A218T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: ATCC BAA-793/NCIMB 8826/WCFS1 / Gene: lp_2219 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q88V64, UniProt: F9UQE3*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 291 K / Method: microbatch under oil
Details: 20% PEG 3350, 0.2M ammonium phosphate, Microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97860, 0.97917, 0.91837
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 1, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.979171
30.918371
ReflectionResolution: 1.963→500 Å / Num. all: 90354 / Num. obs: 87372 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 22.2
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 13.6 / Num. unique all: 9008 / % possible all: 90.4

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.963→31.447 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.178 4393 5.03 %RANDOM
Rwork0.169 ---
obs0.17 87331 96.37 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.721 Å2
Refinement stepCycle: LAST / Resolution: 1.963→31.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5178 0 10 396 5584
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg1.475
X-RAY DIFFRACTIONf_dihedral_angle_d17.343
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0057-0.0030.00190.00420.01680.00770.0364-0.0221-0.0111-0.0166-0.03690.02480.00320.02590-0.00630.00280.0017-0.0072-0.00430.01048.584223.770441.1257
20.00450.00210.00020.0044-0.00480.00780.0260.0105-0.00610.0082-0.0119-0.02130.0082-0.0357-00.0087-0.00460.00330.011-0-0.0005-18.764124.9676-3.0797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 341
2X-RAY DIFFRACTION2chain BB1 - 341

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