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- PDB-1sqe: 1.5A Crystal Structure Of the protein PG130 from Staphylococcus a... -

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Basic information

Entry
Database: PDB / ID: 1sqe
Title1.5A Crystal Structure Of the protein PG130 from Staphylococcus aureus, Structural genomics
Componentshypothetical protein PG130
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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) 2
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 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
DepositionMar 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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Assembly

Deposited unit
A: hypothetical protein PG130
B: hypothetical protein PG130


Theoretical massNumber of molelcules
Total (without water)25,8892
Polymers25,8892
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-12 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.233, 38.013, 61.552
Angle α, β, γ (deg.)90.00, 93.91, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein existed as dimer. MolA and MolB represents the dimer in asymmetric unit.

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Components

#1: Protein hypothetical protein PG130


Mass: 12944.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MU50 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99X56
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.04 Å3/Da / Density % sol: 39.68 %
Description: FRIEDEL PAIRS WERE USED IN DETERMINING THIS STRUCTURE
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 4000, 0.25M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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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: Oct 26, 2003 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97981
30.946561
ReflectionResolution: 1.5→50 Å / Num. all: 65616 / Num. obs: 59383 / % possible obs: 94.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 4.78 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 23.29
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 2.12 / Num. unique all: 2589 / % possible all: 77.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→19.4 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 360920.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: FRIEDEL PAIRS WERE USED IN DETERMINING THIS STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2922 4.9 %RANDOM
Rwork0.203 ---
all0.213 65616 --
obs0.203 59383 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2343 Å2 / ksol: 0.362331 e/Å3
Displacement parametersBiso mean: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å22.31 Å2
2---1.81 Å20 Å2
3---1.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 0 231 1962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.64
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 386 4.9 %
Rwork0.288 7524 -
obs--72.4 %
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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