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- PDB-1p99: 1.7A crystal structure of protein PG110 from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 1p99
Title1.7A crystal structure of protein PG110 from Staphylococcus aureus
ComponentsHypothetical protein PG110
KeywordsStructural genomics / unknown function / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Lipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLYCINE / METHIONINE / : / Lipoprotein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsZhang, R. / Zhou, M. / Joachimiak, G. / Schneewind, O. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Biochemistry / Year: 2004
Title: The membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus binds the dipeptide GlyMet via side chain interactions.
Authors: Williams, W.A. / Zhang, R.G. / Zhou, M. / Joachimiak, G. / Gornicki, P. / Missiakas, D. / Joachimiak, A.
History
DepositionMay 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Hypothetical protein PG110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7373
Polymers32,5131
Non-polymers2242
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.496, 73.883, 92.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein existed as monomer, Chain B (gly-met) is the peptide which naturaly binding to this protein

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Components

#1: Protein Hypothetical protein PG110


Mass: 32512.902 Da / Num. of mol.: 1 / Fragment: Residues 19-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Species: Staphylococcus aureus / Strain: subsp. aureus Mu50 / Gene: SA0422 / Plasmid: PDM 68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 15923454, UniProt: A0A0H3JTG5*PLUS
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM Ammonium Sulfate, 30% pentaerythritol ethoxylate, 50 mM Bis/Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
180 mg/mlprotein1drop
220 mMHEPES-HCl1droppH8.0
3200 mM1dropNaCl
41 mMdithiothreitol1drop
550 mMBis-Tris1reservoirpH6.5
650 mMammonium sulfate1reservoir
727 %pentaerythritol ethoxylate 15/41reservoir

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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: Feb 5, 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: 1.7→50 Å / Num. all: 31444 / Num. obs: 31255 / % possible obs: 99.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 10.45 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 38.87
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.11 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3002 / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.81 Å

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Processing

Software
NameVersionClassification
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 523168.4 / Data cutoff high rms absF: 523168.4 / 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 the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2733 4.9 %RANDOM
Rwork0.2 ---
obs0.2 55440 94.1 %-
all-58916 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.4104 Å2 / ksol: 0.381729 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å20 Å2
2--3.18 Å20 Å2
3----6.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 13 292 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.52
X-RAY DIFFRACTIONc_scangle_it2.42.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 362 4.5 %
Rwork0.305 7699 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Num. reflection obs: 9343

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