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- PDB-3rtl: Staphylococcus aureus heme-bound IsdB-N2 -

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Basic information

Entry
Database: PDB / ID: 3rtl
TitleStaphylococcus aureus heme-bound IsdB-N2
ComponentsIron-regulated surface determinant protein B
KeywordsMETAL TRANSPORT / heme protein / NEAT domain / heme uptake / 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: 1.453 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 3, 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)59,12314
Polymers56,5004
Non-polymers2,62310
Water11,223623
1
A: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7663
Polymers14,1251
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)14,7904
Polymers14,1251
Non-polymers6653
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)14,7663
Polymers14,1251
Non-polymers6412
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)14,8014
Polymers14,1251
Non-polymers6763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Iron-regulated surface determinant protein B
B: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5567
Polymers28,2502
Non-polymers1,3065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-66 kcal/mol
Surface area12640 Å2
MethodPISA
6
C: Iron-regulated surface determinant protein B
D: Iron-regulated surface determinant protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5677
Polymers28,2502
Non-polymers1,3175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-69 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.527, 82.608, 116.888
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: 14125.076 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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
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: Feb 4, 2009 / 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: 1.453→67.42 Å / Num. obs: 97666 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.05 / Χ2: 1.012 / Net I/σ(I): 21.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.453-1.55.70.37392501.03195.2
1.5-1.567.10.28896711.0511100
1.56-1.637.20.20997581.0461100
1.63-1.727.30.15697191.071100
1.72-1.837.30.12197780.9821100
1.83-1.977.30.09697920.9681100
1.97-2.177.40.07597811.0471100
2.17-2.487.40.06398470.9941100
2.48-3.127.40.04799230.9671100
3.12-507.20.035101470.97198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.73 Å33.55 Å
Translation1.73 Å33.55 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0110refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Selenomethionine-labeled IsdB-N2

Resolution: 1.453→67.42 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.156 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 4876 5 %RANDOM
Rwork0.178 ---
obs0.1799 97572 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.8 Å2 / Biso mean: 20.6395 Å2 / Biso min: 5.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2--0.27 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.453→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 178 623 4667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224522
X-RAY DIFFRACTIONr_angle_refined_deg1.3792.1826242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.47724.923195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35515824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2441518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023407
X-RAY DIFFRACTIONr_mcbond_it1.2321.52439
X-RAY DIFFRACTIONr_mcangle_it2.02224030
X-RAY DIFFRACTIONr_scbond_it2.63232083
X-RAY DIFFRACTIONr_scangle_it3.8234.52191
X-RAY DIFFRACTIONr_rigid_bond_restr1.48734522
X-RAY DIFFRACTIONr_sphericity_free6.3683629
X-RAY DIFFRACTIONr_sphericity_bonded4.34234364
LS refinement shellResolution: 1.453→1.491 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 323 -
Rwork0.257 5974 -
all-6297 -
obs--87.48 %

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