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- PDB-2ite: Crystal structure of the IsdA NEAT domain from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 2ite
TitleCrystal structure of the IsdA NEAT domain from Staphylococcus aureus
ComponentsIron-regulated surface determinant protein A
KeywordsMETAL BINDING PROTEIN / NEAT domain / heme / iron
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
Iron-regulated surface determinant protein A / Iron-regulated surface determinant protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsGrigg, J.C. / Vermeiren, C.L. / Heinrichs, D.E. / Murphy, M.E.
CitationJournal: Mol.Microbiol. / Year: 2007
Title: Haem recognition by a Staphylococcus aureus NEAT domain.
Authors: Grigg, J.C. / Vermeiren, C.L. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionOct 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software

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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)29,7813
Polymers29,5742
Non-polymers2071
Water7,008389
1
A: Iron-regulated surface determinant protein A


Theoretical massNumber of molelcules
Total (without water)14,7871
Polymers14,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron-regulated surface determinant protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9942
Polymers14,7871
Non-polymers2071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.428, 58.243, 45.246
Angle α, β, γ (deg.)90.000, 95.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14787.022 Da / Num. of mol.: 2 / Fragment: NEAT Domain (residues 62-184)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: RN6390 / Gene: isdA, frpA, stbA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7A152, UniProt: Q2FZE9*PLUS
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 30% PEG 4000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.97879, 0.97927
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978791
20.979271
Reflection

Χ2: 0.99 / D res high: 1.5 Å / D res low: 50 Å

IDAv σ(I) over netINumberRmerge(I) obsNum. obs% possible obs
113.52211080.073676699.5
215.91622140.0493671299
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
3.235099.710.0470.989
2.563.2310010.080.983
2.242.5699.410.1261.017
2.042.2499.310.0980.996
1.892.0499.310.0840.98
1.781.8999.410.121.005
1.691.7899.310.1630.99
1.621.6999.310.2130.995
1.551.6299.610.2560.983
1.51.5599.310.3230.985
3.235099.820.0330.974
2.563.2310020.0581.007
2.242.5698.720.0540.992
2.042.2499.220.0511.003
1.892.0498.820.0751.009
1.781.899920.1150.989
1.691.7899.220.1650.987
1.621.699920.2260.973
1.551.6299.220.2810.976
1.51.5597.220.3560.993
ReflectionResolution: 1.5→50 Å / Num. obs: 36766 / % possible obs: 99.5 % / Rmerge(I) obs: 0.07 / Χ2: 0.994 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.550.32336280.98599.3
1.55-1.620.25636810.98399.6
1.62-1.690.21336340.99599.3
1.69-1.780.16336690.9999.3
1.78-1.890.1236741.00599.4
1.89-2.040.08436470.9899.3
2.04-2.240.09836680.99699.3
2.24-2.560.12636621.01799.4
2.56-3.230.0837410.983100
3.23-500.04737620.98999.7

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MADD res high: 1.6 Å / D res low: 50 Å / FOM : 0.4 / Reflection: 29984
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength10.97883.84-7.05
12 wavelength20.97933.85-8.32
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se9.1150.5720.9980.2360.511
2Se25.1680.0540.5710.2780.775
3Se14.890.5220.9380.2380.34
4Se15.540.0070.6790.3490.794
5Se22.7050.5340.890.160.334
Phasing MAD shell
Resolution (Å)FOM Reflection
5.82-500.511390
3.65-5.820.542482
2.85-3.650.513194
2.41-2.850.483751
2.13-2.410.444221
1.93-2.130.384642
1.77-1.930.324983
1.65-1.770.265321
Phasing dmFOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0.53 / Reflection: 29984 / Reflection acentric: 28842 / Reflection centric: 1142
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4.6-45.0530.90.920.7813321192140
2.9-4.60.90.910.7940813846235
2.3-2.90.790.790.6450774874203
2-2.30.690.690.5250774909168
1.7-20.490.490.389238667256
1.6-1.70.320.320.1454945354140

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 1.6→45.04 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.647 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1520 5.1 %RANDOM
Rwork0.166 ---
all0.168 ---
obs-29982 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å2-0.01 Å2
2---0.34 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 13 389 2382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222041
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9262771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65125.66106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47515348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.15154
X-RAY DIFFRACTIONr_chiral_restr0.1050.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021562
X-RAY DIFFRACTIONr_nbd_refined0.2120.2925
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.238
X-RAY DIFFRACTIONr_mcbond_it1.0181.51241
X-RAY DIFFRACTIONr_mcangle_it1.56521987
X-RAY DIFFRACTIONr_scbond_it2.8393899
X-RAY DIFFRACTIONr_scangle_it4.2724.5784
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 102 -
Rwork0.173 2061 -
obs-2163 100 %

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