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- PDB-3h04: The crystal structure of the protein with unknown function from S... -

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Basic information

Entry
Database: PDB / ID: 3h04
TitleThe crystal structure of the protein with unknown function from Staphylococcus aureus subsp. aureus Mu50
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / Protein with unknown function / MCSG / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


: / BD-FAE / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BD-FAE-like domain-containing protein / Abhydrolase_3 domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsZhang, R. / Tesar, C. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein with unknown function from Staphylococcus aureus subsp. aureus Mu50
Authors: Zhang, R. / Tesar, C. / Sather, A. / Clancy, S. / Joachimiak, A.
History
DepositionApr 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)31,4141
Polymers31,4141
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.033, 47.033, 404.486
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein uncharacterized protein


Mass: 31413.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: GI:14246089, SAV0321 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99WQ5, UniProt: A0A0H3JX93*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 289 K / pH: 5.1
Details: 0.2M calcium chloride dihydrate, 20% PEG3350, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2008 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 1.9→67.42 Å / Num. obs: 20087 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 35.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3.1 / % possible all: 64.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→67.42 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.153 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.159
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1086 5.1 %RANDOM
Rwork0.196 ---
obs0.198 20087 94 %-
all-21362 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2191 0 0 98 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222253
X-RAY DIFFRACTIONr_bond_other_d0.0010.021497
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9533066
X-RAY DIFFRACTIONr_angle_other_deg0.97533658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83924.404109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60515376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.431511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212504
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9121.51367
X-RAY DIFFRACTIONr_mcbond_other0.2941.5543
X-RAY DIFFRACTIONr_mcangle_it1.59422236
X-RAY DIFFRACTIONr_scbond_it2.6563886
X-RAY DIFFRACTIONr_scangle_it3.8964.5830
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 54 -
Rwork0.181 1006 -
obs--64.79 %
Refinement TLS params.Method: refined / Origin x: 38.068 Å / Origin y: 4.896 Å / Origin z: 16.372 Å
111213212223313233
T0.0609 Å20.0045 Å20.0038 Å2-0.068 Å20.0414 Å2--0.0285 Å2
L0.7368 °2-0.252 °2-0.0821 °2-1.1154 °2-0.2941 °2--2.0459 °2
S0.0283 Å °-0.0027 Å °0.018 Å °0.0394 Å °0.0889 Å °0.0705 Å °-0.0394 Å °-0.0816 Å °-0.1172 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 200
5X-RAY DIFFRACTION1A201 - 240
6X-RAY DIFFRACTION1A241 - 274

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