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- PDB-1oru: Crystal Structure of APC1665, YUAD protein from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1oru
TitleCrystal Structure of APC1665, YUAD protein from Bacillus subtilis
ComponentsyuaD protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YUAD protein / Cytosolic Hypothetical Protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


molybdenum ion binding / catalytic activity / pyridoxal phosphate binding
Similarity search - Function
: / PK beta-barrel domain-like / Molybdenum cofactor sulfurase, C-terminal / MOSC domain / MOSC domain profile. / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase-like, insert domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Putative metal-sulfur cluster biosynthesis proteins YuaD
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKim, Y. / Joachimiak, A. / Edwards, A. / Skarina, T. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of APC1665, YUAD protein from Bacillus subtilis
Authors: Kim, Y. / Joachimiak, A. / Edwards, A. / Skarina, T. / Savchenko, A.
History
DepositionMar 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: yuaD protein
B: yuaD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1658
Polymers43,7712
Non-polymers3956
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-83 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.652, 87.202, 122.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAlthough there is no evicdence, it appears to be a dimer as the asymmetric content.

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Components

#1: Protein yuaD protein


Mass: 21885.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: O32079
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.45 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, PEG 400, Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97943, 0.97962, 0.961
DetectorType: SBC-3 / Detector: CCD / Date: Feb 9, 2003 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979431
20.979621
30.9611
ReflectionResolution: 1.8→43.6 Å / Num. all: 43357 / Num. obs: 43357 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.091
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6 % / Rmerge(I) obs: 0.522 / Num. unique all: 4187 / % possible all: 98

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Processing

Software
NameVersionClassification
CNS1refinement
d*TREKdata reduction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→41.07 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4203 10 %RANDOM
Rwork0.196 ---
all0.198 41997 --
obs0.198 41997 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.6143 Å2 / ksol: 0.377145 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.92 Å20 Å20 Å2
2---5.86 Å20 Å2
3----1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 18 365 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.832.5
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 895 10.4 %
Rwork0.293 5820 -
obs-8039 92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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