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- PDB-2p2e: Crystal structure of a putative Fe-S biosynthesis protein from La... -

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Basic information

Entry
Database: PDB / ID: 2p2e
TitleCrystal structure of a putative Fe-S biosynthesis protein from Lactobacillus salivarius with novel protein fold
ComponentsPutative Fe-S biosynthesis protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / beta-barrel / Fe-S biosynthesis / 10399l / Protein Structure Initiative / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyHypothetical Protein Aq_1857; Chain: A; / HesB-like domain / FeS cluster biogenesis / HesB-like domain superfamily / Iron-sulphur cluster biosynthesis / Sandwich / Mainly Beta / Core domain-containing protein
Function and homology information
Biological speciesLactobacillus salivarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.48 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative Fe-S biosynthesis protein from Lactobacillus salivarius with novel protein fold
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Fe-S biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)14,8271
Polymers14,8271
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.577, 94.577, 36.854
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative Fe-S biosynthesis protein / Putative Fe-S cluster assembly protein


Mass: 14826.751 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus salivarius (bacteria) / Strain: UCC118 / Gene: LSL_1730 / Plasmid: PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL / References: UniProt: Q1WRG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Ammonium acetate, 0.1M Sodium acetate, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2007 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. all: 6368 / Num. obs: 6368 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.4 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.6
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1 / Num. unique all: 352 / % possible all: 52.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.48→47.29 Å / Rfactor Rfree error: 0.019 / Data cutoff high absF: 45461.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 198 3.2 %RANDOM
Rwork0.229 ---
all0.229 6133 --
obs0.229 6133 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.4843 Å2 / ksol: 0.366131 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å24.15 Å20 Å2
2--0.62 Å20 Å2
3----1.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.48→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 0 30 969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.64
LS refinement shellResolution: 2.48→2.64 Å / Rfactor Rfree error: 0.068 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 23 3.7 %
Rwork0.308 594 -
obs--54.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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