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

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Basic information

Entry
Database: PDB / ID: 2qgo
TitleCrystal structure of a putative Fe-S biosynthesis protein from Lactobacillus acidophilus
ComponentsPutative Fe-S biosynthesis protein
KeywordsBIOSYNTHETIC PROTEIN / PSI-2 / NYSGXRC / 10399g / Fe-S cluster protein / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
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 acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structural analysis of Fe-S cluster proteins.
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.3Feb 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

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Assembly

Deposited unit
A: Putative Fe-S biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)15,5531
Polymers15,5531
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.261, 61.261, 40.442
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Putative Fe-S biosynthesis protein


Mass: 15552.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Strain: NCFM / Gene: LBA0486 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL / References: UniProt: Q5FLQ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 298 K / pH: 7 / Details: 1.8M Ammonium citrate, pH 7.0, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 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: 2.04→50 Å / Num. obs: 17922 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.4
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 2 / % possible all: 73

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→29.56 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 75670.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used for phasing. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of ...Details: The Friedel pairs were used for phasing. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 512 2.9 %RANDOM
Rwork0.226 ---
obs0.226 17469 93.9 %-
all-9419 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.569 Å2 / ksol: 0.36202 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20 Å20 Å2
2--1.94 Å20 Å2
3----3.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.04→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 0 29 915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 62 2.8 %
Rwork0.253 2140 -
obs--71.9 %
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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