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- PDB-2e7d: Crystal structure of a NEAT domain from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 2e7d
TitleCrystal structure of a NEAT domain from Staphylococcus aureus
ComponentsHypothetical protein IsdHHypothesis
KeywordsMETAL BINDING PROTEIN / Ig-like fold
Function / homology
Function and homology information


heme binding / extracellular region
Similarity search - Function
Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide ...Iron-regulated surface determinant protein H / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Iron-regulated surface determinant protein H
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSuenaga, A. / Tanaka, Y. / Yao, M. / Kumagai, I. / Tanaka, I. / Tsumoto, K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus
Authors: Watanabe, M. / Tanaka, Y. / Suenaga, A. / Kuroda, M. / Yao, M. / Watanabe, N. / Arisaka, F. / Ohta, T. / Tanaka, I. / Tsumoto, K.
History
DepositionJan 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Hypothetical protein IsdH
B: Hypothetical protein IsdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2408
Polymers29,7092
Non-polymers5316
Water1,67593
1
A: Hypothetical protein IsdH
B: Hypothetical protein IsdH
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)181,44248
Polymers178,25412
Non-polymers3,18936
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area33560 Å2
ΔGint-362 kcal/mol
Surface area56080 Å2
MethodPISA
2
A: Hypothetical protein IsdH
B: Hypothetical protein IsdH
hetero molecules

A: Hypothetical protein IsdH
B: Hypothetical protein IsdH
hetero molecules

A: Hypothetical protein IsdH
B: Hypothetical protein IsdH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,72124
Polymers89,1276
Non-polymers1,59418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12910 Å2
ΔGint-157 kcal/mol
Surface area31910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.247, 124.247, 119.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hypothetical protein IsdH / Hypothesis / heme binding protein


Mass: 14854.489 Da / Num. of mol.: 2 / Fragment: NEAT domain, residue 539-664
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: IsdH / Plasmid: pDBHT3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q931P4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.25
Details: 0.1M sodium acetate, 2.2M ammonium sulfate, pH 4.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A11
SYNCHROTRONPhoton Factory BL-5A20.97945, 0.97955, 0.96432
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 14, 2006
ADSC QUANTUM 3152CCDMay 23, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979451
30.979551
40.964321
ReflectionResolution: 2.2→50 Å / Num. obs: 18212 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.042
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.6 % / Rsym value: 0.343 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2476559.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1785 9.8 %RANDOM
Rwork0.24 ---
obs0.24 18159 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.6784 Å2 / ksol: 0.352619 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å22.75 Å20 Å2
2---0.85 Å20 Å2
3---1.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 31 93 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 281 9.3 %
Rwork0.279 2728 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligand.paramligand.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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