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- PDB-2o6p: Crystal Structure of the heme-IsdC complex -

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Basic information

Entry
Database: PDB / ID: 2o6p
TitleCrystal Structure of the heme-IsdC complex
ComponentsIron-regulated surface determinant protein C
KeywordsTRANSPORT PROTEIN / Beta barrel / protein-heme complex
Function / homology
Function and homology information


heme transport / hemoglobin binding / peptidoglycan-based cell wall / extracellular region / metal ion binding
Similarity search - Function
Sortase B signal domain, NPQTN class / Haem uptake protein IsdC / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Iron-regulated surface determinant protein C / Iron-regulated surface determinant protein C
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsSharp, K.H. / Schneider, S. / Cockayne, A. / Paoli, M.
CitationJournal: J. Biol. Chem. / Year: 2007
Title: Crystal structure of the heme-IsdC complex, the central conduit of the Isd iron/heme uptake system in Staphylococcus aureus.
Authors: Sharp, K.H. / Schneider, S. / Cockayne, A. / Paoli, M.
History
DepositionDec 8, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Dec 13, 2017Group: Advisory / Database references / Category: citation / pdbx_unobs_or_zero_occ_residues
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Iron-regulated surface determinant protein C
B: Iron-regulated surface determinant protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,31912
Polymers35,6232
Non-polymers1,69610
Water3,405189
1
A: Iron-regulated surface determinant protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5945
Polymers17,8111
Non-polymers7834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Iron-regulated surface determinant protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7257
Polymers17,8111
Non-polymers9146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-236 kcal/mol
Surface area12580 Å2
MethodPISA
4
A: Iron-regulated surface determinant protein C
hetero molecules

B: Iron-regulated surface determinant protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,31912
Polymers35,6232
Non-polymers1,69610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area2970 Å2
ΔGint-213 kcal/mol
Surface area13800 Å2
MethodPISA
5
A: Iron-regulated surface determinant protein C
hetero molecules

B: Iron-regulated surface determinant protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,31912
Polymers35,6232
Non-polymers1,69610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_435x-1/2,-y-3/2,-z1
Buried area2960 Å2
ΔGint-206 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.489, 70.441, 88.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Iron-regulated surface determinant protein C / IsdC / Staphylococcal iron-regulated protein D


Mass: 17811.355 Da / Num. of mol.: 2 / Fragment: residues 28-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: N315 / Plasmid: pGAT2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7A654, UniProt: Q8KQR1*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: IsdC at 95mg/ml in 50mM Tris-HCl pH 8.0, 500mM NaCl mixed in equal volumes (2 + 2 l) with reservoir solution containing 26% PEG 550, MME, 18mM zinc sulphate, 0.1M MES pH 6.0, VAPOR ...Details: IsdC at 95mg/ml in 50mM Tris-HCl pH 8.0, 500mM NaCl mixed in equal volumes (2 + 2 l) with reservoir solution containing 26% PEG 550, MME, 18mM zinc sulphate, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933, 1.739, 1.741, 1.722
DetectorDate: Aug 31, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
21.7391
31.7411
41.7221
ReflectionResolution: 1.5→47.5 Å / Num. all: 48228 / Num. obs: 45711 / Redundancy: 4.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.3
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6918

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→35.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.204 / SU ML: 0.054 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22204 2433 5.1 %RANDOM
Rwork0.19343 ---
obs0.19487 45711 99.71 %-
all-48228 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.346 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 94 189 2243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222169
X-RAY DIFFRACTIONr_angle_refined_deg1.4442.0552977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36625.728103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03315385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.099152
X-RAY DIFFRACTIONr_chiral_restr0.0780.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021666
X-RAY DIFFRACTIONr_nbd_refined0.1930.2884
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2166
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0770.23
X-RAY DIFFRACTIONr_mcbond_it0.9541.51270
X-RAY DIFFRACTIONr_mcangle_it1.35522006
X-RAY DIFFRACTIONr_scbond_it2.46231057
X-RAY DIFFRACTIONr_scangle_it2.8794.5951
X-RAY DIFFRACTIONr_rigid_bond_restr2.06832327
X-RAY DIFFRACTIONr_sphericity_free3.953200
X-RAY DIFFRACTIONr_sphericity_bonded2.71832093
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 176 -
Rwork0.338 3270 -
obs-6918 98.46 %

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