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- PDB-3hl6: Staphylococcus aureus pathogenicity island 3 ORF9 protein -

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Basic information

Entry
Database: PDB / ID: 3hl6
TitleStaphylococcus aureus pathogenicity island 3 ORF9 protein
ComponentsPathogenicity island protein
KeywordsUNKNOWN FUNCTION / Staphylococcus aureus / pathogenicity island
Function / homology
Function and homology information


Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #700 / Putative mobile pathogenicity island, N-terminal domain / Putative mobile pathogenicity island / Putative mobile pathogenicity island, N-terminal domain / Putative mobile pathogenicity island / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Pathogenicity island protein / Pathogenicity island protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.5 Å
AuthorsKruse, A.C. / Huseby, M. / Shi, K. / Digre, J. / Schlievert, P.M. / Ohlendorf, D.H. / Earhart, C.A.
CitationJournal: To be Published
Title: Structural and functional studies of a pathogenicity island protein from Staphylococcus aureus
Authors: Kruse, A.C. / Huseby, M. / Shi, K. / Digre, J. / Schlievert, P.M. / Ohlendorf, D.H. / Earhart, C.A.
History
DepositionMay 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 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: Pathogenicity island protein
B: Pathogenicity island protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9154
Polymers51,8442
Non-polymers712
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-29 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.739, 78.578, 83.541
Angle α, β, γ (deg.)90.00, 107.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Pathogenicity island protein


Mass: 25922.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: SACOL0900 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HHI6, UniProt: A0A0H2WYW3*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3 M sodium nitrate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 13, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 17190 / Num. obs: 17190 / % possible obs: 96.7 % / Redundancy: 3.5 % / Rsym value: 0.043 / Net I/σ(I): 22.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 730 / Rsym value: 0.391 / % possible all: 83.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.539 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27638 889 5.2 %RANDOM
Rwork0.22776 ---
obs0.23043 16293 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.175 Å2
Baniso -1Baniso -2Baniso -3
1-4.59 Å20 Å2-4.4 Å2
2---1.94 Å20 Å2
3----5.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 2 58 3143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223141
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9754238
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6045377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56825.065154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.76715573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.1891512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022352
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2940.31417
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.52182
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.5190
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.353
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3380.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8931.51893
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67423054
X-RAY DIFFRACTIONr_scbond_it1.98231248
X-RAY DIFFRACTIONr_scangle_it3.3154.51184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 45 -
Rwork0.337 1041 -
obs--84.45 %

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