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- PDB-3eiw: Crystal structure of Staphylococcus aureus lipoprotein, HtsA -

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Basic information

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


iron coordination entity transport / outer membrane-bounded periplasmic space
Similarity search - Function
: / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HtsA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3952
Polymers33,3591
Non-polymers351
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.703, 43.571, 75.712
Angle α, β, γ (deg.)90.00, 100.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HtsA protein


Mass: 33359.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His6-tag
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.: 382 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
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: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2007
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror.
RadiationMonochromator: a double crystal monochromator (DCM) with an indirectly cryo-cooled first crystal and sagittally focusing second crystal, and vertically focussing mirror (VFM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 36952 / % possible obs: 96.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 20.809
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.662.60.166176.5
1.66-1.723.10.158192.4
1.72-1.83.50.137199.9
1.8-1.93.50.109199.9
1.9-2.023.50.085199.9
2.02-2.173.50.0711100
2.17-2.393.50.0621100
2.39-2.743.50.0551100
2.74-3.453.50.055199.9
3.45-503.40.042199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.74 Å26.13 Å
Translation1.74 Å26.13 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.399 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20001 1845 5 %RANDOM
Rwork0.16329 ---
obs0.16511 35032 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.951 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.81 Å2
2---0.18 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 1 382 2699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222446
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.9863297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2425311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15425.701107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16415503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2961512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021803
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21181
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21709
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.257
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9321.51561
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50322463
X-RAY DIFFRACTIONr_scbond_it2.4493979
X-RAY DIFFRACTIONr_scangle_it3.9184.5834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 102 -
Rwork0.183 1979 -
obs--74.72 %

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