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- PDB-3qzo: Staphylococcus aureus IsdA NEAT domain in complex with heme, redu... -

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Basic information

Entry
Database: PDB / ID: 3qzo
TitleStaphylococcus aureus IsdA NEAT domain in complex with heme, reduced crystal
ComponentsIron-regulated surface determinant protein A
KeywordsMETAL BINDING PROTEIN / heme / transport / iron / uptake / receptor / cell wall / ferrous
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 FE / Iron-regulated surface determinant protein A
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.952 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_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_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_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_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_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
C: Iron-regulated surface determinant protein A
D: Iron-regulated surface determinant protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,23510
Polymers58,5854
Non-polymers2,6506
Water7,476415
1
A: Iron-regulated surface determinant protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2632
Polymers14,6461
Non-polymers6161
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)15,2632
Polymers14,6461
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Iron-regulated surface determinant protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3553
Polymers14,6461
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Iron-regulated surface determinant protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3553
Polymers14,6461
Non-polymers7092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.041, 58.592, 97.834
Angle α, β, γ (deg.)90.000, 92.980, 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: 14646.335 Da / Num. of mol.: 4 / 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES, 30% PEG 6000, pH 6.5, 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: 1.95→40 Å / Num. obs: 45601 / % possible obs: 98.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.013 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.022.80.37740401.05187.9
2.02-2.13.10.33744491.024197.2
2.1-2.23.50.28845921.059199.8
2.2-2.313.70.25146191.072199.9
2.31-2.463.80.246211.0161100
2.46-2.653.80.15946121.0081100
2.65-2.913.80.10546110.9161100
2.91-3.333.80.06446370.8971100
3.33-4.23.80.05246601.0491100
4.2-403.70.03347601.066199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.3 Å30.6 Å
Translation2.3 Å30.6 Å

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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: 1.952→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.837 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 2313 5.1 %RANDOM
Rwork0.1937 ---
obs0.1963 45582 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.29 Å2 / Biso mean: 30.0321 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20.14 Å2
2---1.68 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.952→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3998 0 184 415 4597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224558
X-RAY DIFFRACTIONr_angle_refined_deg1.3712.1586308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.21425.76217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34215715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.471158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213568
X-RAY DIFFRACTIONr_mcbond_it0.7431.52489
X-RAY DIFFRACTIONr_mcangle_it1.34724077
X-RAY DIFFRACTIONr_scbond_it1.89632069
X-RAY DIFFRACTIONr_scangle_it2.9264.52231
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 148 -
Rwork0.282 2786 -
all-2934 -
obs--86.52 %

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