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- PDB-1xbw: 1.9A Crystal Structure of the protein isdG from Staphylococcus au... -

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Basic information

Entry
Database: PDB / ID: 1xbw
Title1.9A Crystal Structure of the protein isdG from Staphylococcus aureus aureus, Structural genomics, MCSG
Componentshypothetical protein isdG
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / MCSG / staphylococcus aureus / protein isdG / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


heme oxygenase (staphylobilin-producing) / iron import into cell / heme oxygenase (decyclizing) activity / heme catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Heme oxygenase IsdG / : / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Heme oxygenase (staphylobilin-producing) 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsZhang, R. / Wu, R. / Joachimiak, G. / Schneewind, O. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Staphylococcus aureus IsdG and IsdI, heme-degrading enzymes with structural similarity to monooxygenases.
Authors: Wu, R. / Skaar, E.P. / Zhang, R. / Joachimiak, G. / Gornicki, P. / Schneewind, O. / Joachimiak, A.
History
DepositionAug 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein isdG
B: hypothetical protein isdG
C: hypothetical protein isdG
D: hypothetical protein isdG


Theoretical massNumber of molelcules
Total (without water)51,1824
Polymers51,1824
Non-polymers00
Water3,549197
1
A: hypothetical protein isdG
B: hypothetical protein isdG


Theoretical massNumber of molelcules
Total (without water)25,5912
Polymers25,5912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-20 kcal/mol
Surface area10320 Å2
MethodPISA
2
C: hypothetical protein isdG
D: hypothetical protein isdG


Theoretical massNumber of molelcules
Total (without water)25,5912
Polymers25,5912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-21 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.742, 66.779, 67.678
Angle α, β, γ (deg.)90.00, 105.18, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein existed as dimer. MolA plus MolB, MolC plus MolD represent two dimers in asymmetric unit

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Components

#1: Protein
hypothetical protein isdG


Mass: 12795.507 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Gene: GI:1003130 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NX62
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.294 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG, 0.1M Bis-tris, 0.2M NH4SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9798, 0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Jul 22, 2003 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.946561
ReflectionResolution: 1.9→50 Å / Num. obs: 66916 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 29.24
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 4.02 / Num. unique all: 2166 / % possible all: 61.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→32.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 428884.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3151 4.9 %RANDOM
Rwork0.23 ---
obs0.23 63987 92.7 %-
all-69026 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.0323 Å2 / ksol: 0.406194 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.73 Å20 Å22.89 Å2
2---1.69 Å20 Å2
3----7.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 0 197 3352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 462 4.7 %
Rwork0.33 9275 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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