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- PDB-2q8p: Crystal Structure of selenomethionine labelled S. aureus IsdE com... -

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Basic information

Entry
Database: PDB / ID: 2q8p
TitleCrystal Structure of selenomethionine labelled S. aureus IsdE complexed with heme
ComponentsIron-regulated surface determinant E
KeywordsMETAL TRANSPORT / helical backbone metal receptor superfamily
Function / homology
Function and homology information


heme transport / heme binding / metal ion binding / plasma membrane
Similarity search - Function
ABC transporter, high-affinity heme uptake system protein IsdE / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / High-affinity heme uptake system protein IsdE
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.95 Å
AuthorsGrigg, J.C. / Murphy, M.E.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Heme Coordination by Staphylococcus aureus IsdE.
Authors: Grigg, J.C. / Vermeiren, C.L. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionJun 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-regulated surface determinant E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7292
Polymers30,1121
Non-polymers6161
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.527, 63.527, 144.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Iron-regulated surface determinant E


Mass: 30112.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: N315 / Gene: isdE / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7A652
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM MES, 0.2 M ammonuim acetate, 28% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.978894 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 19, 2007
Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978894 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 19425 / % possible obs: 86 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 30
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.95-2.027.60.359179
2.02-2.17.90.268185.6
2.1-2.27.90.192185
2.2-2.317.90.15186.8
2.31-2.4615.20.167186.7
2.46-2.65150.122186.8
2.65-2.9114.70.095187.2
2.91-3.3314.50.069186.3
3.33-4.214.40.055185.4
4.2-5014.50.059190.9

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.1 Å / D res low: 10 Å / FOM : 0.37 / Reflection: 15694
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
124.1034.2110.179SE34.90.87
250.49528.5458.208SE35.60.75
326.58212.4086.436SE36.50.88
452.73719.21912.642SE32.30.72
514.4883.95311.834SE34.30.63
653.07935.8099.737SE38.40.58
749.00613.8673.957SE600.74
851.97947.90414.533SE53.10.76
941.40123.3866.734SE53.70.51
Phasing MAD shell
Resolution (Å)FOM Reflection
6.34-100.431110
4.42-6.340.461565
3.58-4.420.441891
3.08-3.580.422104
2.75-3.080.42183
2.51-2.750.372170
2.32-2.510.292265
2.17-2.320.212406
Phasing dmFOM : 0.62 / FOM acentric: 0.64 / FOM centric: 0.55 / Reflection: 15694 / Reflection acentric: 12992 / Reflection centric: 2702
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-9.9990.910.940.85674437237
3.8-60.920.940.8324571879578
3-3.80.820.860.6829522412540
2.6-30.640.670.4827352309426
2.3-2.60.460.490.342873689598
2.1-2.30.290.30.225892266323

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.11phasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.493 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26293 963 5.1 %RANDOM
Rwork0.20105 ---
obs0.20422 17938 84.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.785 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 43 183 2302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222169
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.392.0412939
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4155257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10325.91493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49715414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.514155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021601
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.21035
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21471
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0370.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7541.51336
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07222104
X-RAY DIFFRACTIONr_scbond_it1.9943949
X-RAY DIFFRACTIONr_scangle_it2.7724.5833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 59 -
Rwork0.262 1235 -
obs--80.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.02880.06191.31962.7294-0.28824.195-0.30290.03860.1318-0.03680.067-0.2829-0.26540.53060.2360.1389-0.0103-0.05290.07560.011-0.045968.27149.04359.878
22.0160.31540.43432.35890.08243.0929-0.1520.2207-0.0982-0.17560.0852-0.25610.20920.54780.06670.1050.06160.01090.0829-0.0084-0.082369.36341.38156.084
31.35270.44430.04951.2716-0.14223.3746-0.1714-0.0456-0.16740.07930.04250.15870.1211-0.26560.12890.16770.02990.0477-0.0108-0.0358-0.016545.25334.78658.19
43.33650.83680.62060.8296-1.32463.6509-0.22080.1234-0.36290.01120.03750.06270.3194-0.09020.18320.2343-0.01030.0361-0.0479-0.0731-0.004147.68431.45951.213
51.97491.0062-1.59322.1524-0.62022.057-0.30260.6881-0.0526-0.10030.20620.3533-0.0357-0.45420.09640.1406-0.0305-0.05340.1199-0.09120.010240.5235.82546.978
62.16020.69190.26561.77340.07723.7522-0.16050.10550.197-0.01720.04680.332-0.3097-0.32970.11370.15970.0453-0.018-0.0264-0.038-0.0141.67443.92751.658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 673 - 38
2X-RAY DIFFRACTION2AA68 - 14939 - 120
3X-RAY DIFFRACTION3AA150 - 187121 - 158
4X-RAY DIFFRACTION4AA188 - 212159 - 183
5X-RAY DIFFRACTION5AA213 - 229184 - 200
6X-RAY DIFFRACTION6AA230 - 289201 - 260

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