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- PDB-3qzp: Staphylococcus aureus IsdA NEAT domain in complex with cobalt-pro... -

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Basic information

Entry
Database: PDB / ID: 3qzp
TitleStaphylococcus aureus IsdA NEAT domain in complex with cobalt-protoporphyrin IX
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 - #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 CO / Iron-regulated surface determinant protein A
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 1.3Sep 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_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_alt_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.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_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

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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)30,9048
Polymers29,2932
Non-polymers1,6116
Water5,224290
1
A: Iron-regulated surface determinant protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3583
Polymers14,6461
Non-polymers7122
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)15,5465
Polymers14,6461
Non-polymers9004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.465, 51.707, 55.747
Angle α, β, γ (deg.)90.000, 92.080, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

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


Mass: 14646.335 Da / Num. of mol.: 2 / Fragment: UNP Residues 62-184
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-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 1.5 M ammonium sulfate, 0.1 M citrate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 12, 2007 / Details: Vertically focusing mirror
RadiationMonochromator: Double Crystal Monochromator (ACCEL DCM) with an indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22960 / % possible obs: 96.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.091 / Χ2: 0.998 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.932.50.3419210.993178.1
1.93-1.972.80.27511010.974194
1.97-2.012.90.26811261.031195.7
2.01-2.0530.24811471.04196.6
2.05-2.093.10.2111431.014196.5
2.09-2.143.20.19711361.014197.1
2.14-2.193.30.18511210.98196.2
2.19-2.253.30.16611721.006198.3
2.25-2.323.30.18711530.996197.3
2.32-2.393.40.16911511.024197.2
2.39-2.483.40.1511560.978198.3
2.48-2.583.40.14411590.926198.1
2.58-2.73.50.13311791.026198
2.7-2.843.60.11211611.002198
2.84-3.023.60.10911661.029198.5
3.02-3.253.70.07711860.972198.5
3.25-3.583.70.05811671.003198.6
3.58-4.093.60.05411890.986198.8
4.09-5.163.60.04112010.962199.3
5.16-503.50.04112251.02198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0109refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ITF

2itf


Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.111 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 1174 5.1 %RANDOM
Rwork0.1782 ---
obs0.1805 22863 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.56 Å2 / Biso mean: 17.6374 Å2 / Biso min: 4.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å2-0.84 Å2
2---0.87 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 109 290 2435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212426
X-RAY DIFFRACTIONr_angle_refined_deg2.9342.0283363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6225.913115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36815384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.335154
X-RAY DIFFRACTIONr_chiral_restr0.430.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211920
X-RAY DIFFRACTIONr_mcbond_it0.721.51331
X-RAY DIFFRACTIONr_mcangle_it1.34622193
X-RAY DIFFRACTIONr_scbond_it1.76431095
X-RAY DIFFRACTIONr_scangle_it2.8584.51170
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 79 -
Rwork0.215 1375 -
all-1454 -
obs--83.13 %

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