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- PDB-3rur: Staphylococcus aureus heme-bound selenomethionine-labeled IsdB-N2 -

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Basic information

Entry
Database: PDB / ID: 3rur
TitleStaphylococcus aureus heme-bound selenomethionine-labeled IsdB-N2
ComponentsIron-regulated surface determinant protein B
KeywordsMETAL TRANSPORT / heme protein / heme uptake / NEAT domain / heme binding / cell wall
Function / homology
Function and homology information


heme transmembrane transporter activity / extracellular region / metal ion binding
Similarity search - Function
Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide ...Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Iron-regulated surface determinant protein B
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsGaudin, C.F.M. / Grigg, J.C. / Arrieta, A.L. / Murphy, M.E.P.
CitationJournal: Biochemistry / Year: 2011
Title: Unique Heme-Iron Coordination by the Hemoglobin Receptor IsdB of Staphylococcus aureus.
Authors: Gaudin, C.F. / Grigg, J.C. / Arrieta, A.L. / Murphy, M.E.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-regulated surface determinant protein B
B: Iron-regulated surface determinant protein B
C: Iron-regulated surface determinant protein B
D: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,40113
Polymers57,8134
Non-polymers2,5879
Water9,530529
1
A: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0943
Polymers14,4531
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0943
Polymers14,4531
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1184
Polymers14,4531
Non-polymers6653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0943
Polymers14,4531
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Iron-regulated surface determinant protein B
D: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1886
Polymers28,9072
Non-polymers1,2824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-66 kcal/mol
Surface area12200 Å2
MethodPISA
6
B: Iron-regulated surface determinant protein B
C: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2137
Polymers28,9072
Non-polymers1,3065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-63 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.814, 79.378, 113.869
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Iron-regulated surface determinant protein B / Fur-regulated protein B / Staphylococcal iron-regulated protein H / Staphylococcus aureus surface protein J


Mass: 14453.342 Da / Num. of mol.: 4 / Fragment: NEAT domain (UNP Residues 341-459)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: frpB, isdB, SA0976, sasJ, sirH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7A656
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, 25% PEG 3350, 0.1 M MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 30, 2008 / Details: Rh coated flat mirror; toroidal focusing mirror
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 53106 / % possible obs: 99.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.049 / Χ2: 1.013 / Net I/σ(I): 20.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.763.70.3150241.093195.5
1.76-1.834.70.25252321.053199.4
1.83-1.914.70.22852431.086199.5
1.91-2.024.70.16452861.035199.6
2.02-2.144.70.12252861.046199.8
2.14-2.314.70.10253090.982199.9
2.31-2.544.80.07453520.9851100
2.54-2.914.80.05753650.9921100
2.91-3.664.70.03954110.92199.9
3.66-504.50.02855980.969198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.97 Å37.61 Å
Translation1.97 Å37.61 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0110refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2e7d

2e7d


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.477 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 2697 5.1 %RANDOM
Rwork0.193 ---
obs0.195 53042 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.39 Å2 / Biso mean: 28.0491 Å2 / Biso min: 12.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 177 529 4526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224220
X-RAY DIFFRACTIONr_angle_refined_deg1.4792.0745762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5195495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.95825192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58415795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9671516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023152
X-RAY DIFFRACTIONr_mcbond_it0.891.52378
X-RAY DIFFRACTIONr_mcangle_it1.64523918
X-RAY DIFFRACTIONr_scbond_it2.731842
X-RAY DIFFRACTIONr_scangle_it4.0754.51833
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 174 -
Rwork0.267 3500 -
all-3674 -
obs--94.33 %

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