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- PDB-3eix: Crystal structure of selenomethionine labelled Staphylococcus aur... -

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Basic information

Entry
Database: PDB / ID: 3eix
TitleCrystal structure of selenomethionine labelled Staphylococcus aureus lipoprotein, HtsA
ComponentsHtsA protein
KeywordsTRANSPORT PROTEIN / siderophore / lipoprotein / heme / haem
Function / homology
Function and homology information


ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SA1979 protein / Similar to ferrichrome ABC transporter
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsGrigg, J.C. / Murphy, M.E.P.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Characterization of staphyloferrin A biosynthetic and transport mutants in Staphylococcus aureus.
Authors: Beasley, F.C. / Vines, E.D. / Grigg, J.C. / Zheng, Q. / Liu, S. / Lajoie, G.A. / Murphy, M.E. / Heinrichs, D.E.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HtsA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5822
Polymers33,5471
Non-polymers351
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.952, 43.645, 76.040
Angle α, β, γ (deg.)90.00, 100.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HtsA protein


Mass: 33546.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: htsA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99S89, UniProt: A0A0H3JM89*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 Hepes pH 7.0, Jeffamine ED-2001, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97607 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 6, 2008
Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing)
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 62441 / % possible obs: 97.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.924
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.35-1.42.50.166187.3
1.4-1.453.30.153198.4
1.45-1.523.50.126199.9
1.52-1.63.60.106199.8
1.6-1.73.60.091199.7
1.7-1.833.60.074199.7
1.83-2.023.60.058199.4
2.02-2.313.60.05199.3
2.31-2.913.50.046198.9
2.91-503.40.036196.5

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se9.1510.3450.50.2211.051
2Se15.2480.50.3190.1510.978
3Se9.8940.2810.650.1921.022

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.11phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.352 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16579 3156 5.1 %RANDOM
Rwork0.1294 ---
obs0.13122 59259 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.468 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.38 Å2
2--0.07 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 1 494 2793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222513
X-RAY DIFFRACTIONr_bond_other_d0.0010.021787
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9863398
X-RAY DIFFRACTIONr_angle_other_deg0.93534424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07725.78109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17615521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4641512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022816
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02450
X-RAY DIFFRACTIONr_nbd_refined0.2320.2528
X-RAY DIFFRACTIONr_nbd_other0.1860.21887
X-RAY DIFFRACTIONr_nbtor_refined0.170.21241
X-RAY DIFFRACTIONr_nbtor_other0.0830.21220
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6491.51985
X-RAY DIFFRACTIONr_mcbond_other0.6161.5623
X-RAY DIFFRACTIONr_mcangle_it1.95922544
X-RAY DIFFRACTIONr_scbond_it3.2431085
X-RAY DIFFRACTIONr_scangle_it4.2484.5854
X-RAY DIFFRACTIONr_rigid_bond_restr1.88335070
X-RAY DIFFRACTIONr_sphericity_free7.0053495
X-RAY DIFFRACTIONr_sphericity_bonded3.7734250
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 193 -
Rwork0.142 3669 -
obs--82.7 %

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