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- PDB-1q8b: Structural Genomics, protein YJCS -

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Basic information

Entry
Database: PDB / ID: 1q8b
TitleStructural Genomics, protein YJCS
ComponentsProtein yjcS
KeywordsStructural Genomics / Unknown Function / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / 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
Uncharacterized protein YjcS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsZhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.9A crystal structure of protein YJCS from Bacillus subtilis
Authors: Zhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein yjcS


Theoretical massNumber of molelcules
Total (without water)12,8051
Polymers12,8051
Non-polymers00
Water2,162120
1
A: Protein yjcS

A: Protein yjcS


Theoretical massNumber of molelcules
Total (without water)25,6092
Polymers25,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
2
A: Protein yjcS

A: Protein yjcS


Theoretical massNumber of molelcules
Total (without water)25,6092
Polymers25,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
Buried area1640 Å2
ΔGint-15 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.095, 71.095, 149.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsThis protein exists as dimer which related by the crystallographic 2-fold axis.

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Components

#1: Protein Protein yjcS


Mass: 12804.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: YJCS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: O31641
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.59 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9797, 0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Jun 3, 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
20.97971
30.946561
ReflectionResolution: 1.9→50 Å / Num. all: 11760 / Num. obs: 10996 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 13.04 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 30.54
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.76 / Num. unique all: 1104 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→31.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 552905.79 / Data cutoff high rms absF: 552905.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Freidel pairs were used in the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 991 4.9 %RANDOM
Rwork0.207 ---
obs0.207 20253 91.2 %-
all-22207 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.4281 Å2 / ksol: 0.400777 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-3 Å22.25 Å20 Å2
2--3 Å20 Å2
3----6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms783 0 0 120 903
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it0.791.5
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.352.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 159 5 %
Rwork0.28 3051 -
obs--86.7 %
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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