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- PDB-3qzm: Staphylococcus aureus IsdA NEAT domain H83A variant in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3qzm
TitleStaphylococcus aureus IsdA NEAT domain H83A variant in complex with heme
ComponentsIron-regulated surface determinant protein A
KeywordsMETAL BINDING PROTEIN / heme / transport / iron / uptake / receptor / cell wall
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like ...Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / 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 A
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsGrigg, J.C. / Mao, C.X. / Murphy, M.E.P.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Iron-Coordinating Tyrosine Is a Key Determinant of NEAT Domain Heme Transfer.
Authors: Grigg, J.C. / Mao, C.X. / Murphy, M.E.
History
DepositionMar 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 A
B: Iron-regulated surface determinant protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,59717
Polymers29,1592
Non-polymers2,43815
Water4,594255
1
A: Iron-regulated surface determinant protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8489
Polymers14,5791
Non-polymers1,2698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron-regulated surface determinant protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7488
Polymers14,5791
Non-polymers1,1697
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.490, 51.760, 55.690
Angle α, β, γ (deg.)90.000, 91.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Iron-regulated surface determinant protein A / Fur-regulated protein A / Staphylococcal transferrin-binding protein A


Mass: 14579.265 Da / Num. of mol.: 2 / Fragment: UNP Residues 62-184 / Mutation: H83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: frpA, isdA, SA0977, stbA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7A655
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2010
Details: Sample to detector distance: 107 to 650 mm; Maximum vertical offset: 75mm
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: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→55.658 Å / Num. all: 80164 / Num. obs: 80164 / % possible obs: 97.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 9 Å2 / Rsym value: 0.046 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.25-1.322.50.141526283103880.14187
1.32-1.43.50.1255.638921112780.12599.6
1.4-1.493.50.0976.937566106410.09799.8
1.49-1.613.50.0768.53509599070.07699.6
1.61-1.773.60.0689.53236491160.06899.6
1.77-1.983.50.0511.92918182550.0599.4
1.98-2.283.50.04313.82568573020.04399.2
2.28-2.83.40.04612.52108061320.04698.7
2.8-3.953.30.03418.71549146670.03497.1
3.95-31.0653.30.02822.7825824780.02891.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ITF

2itf


Resolution: 1.25→55.658 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 0.928 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.164 4026 5 %RANDOM
Rwork0.1388 ---
obs0.1401 80088 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.65 Å2 / Biso mean: 12.5754 Å2 / Biso min: 4.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.52 Å2
2---0.01 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.25→55.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 162 255 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222511
X-RAY DIFFRACTIONr_angle_refined_deg1.6762.1633461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.025282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.90226.036111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80915405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.873154
X-RAY DIFFRACTIONr_chiral_restr0.10.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211922
X-RAY DIFFRACTIONr_mcbond_it1.6961.51368
X-RAY DIFFRACTIONr_mcangle_it2.71222253
X-RAY DIFFRACTIONr_scbond_it3.55931143
X-RAY DIFFRACTIONr_scangle_it5.0364.51208
X-RAY DIFFRACTIONr_rigid_bond_restr1.62832511
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 257 -
Rwork0.165 4607 -
all-4864 -
obs--80.78 %

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