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- PDB-3s9x: High resolution crystal structure of ASCH domain from Lactobacill... -

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Basic information

Entry
Database: PDB / ID: 3s9x
TitleHigh resolution crystal structure of ASCH domain from Lactobacillus crispatus JV V101
ComponentsASCH domain
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homologySulfate adenylyltransferase / Sulfate adenylyltransferase / Roll / Alpha Beta
Function and homology information
Biological speciesVibrio cholerae TMA 21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsNocek, B. / Xu, X. / Cui, H. / Jedrzejczak, R. / Edwards, A. / Savchenko, A. / Mabbutt, B.C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: High resolution crystal structure of ASCH domain from Lactobacillus crispatus JV V101
Authors: Nocek, B. / Xu, X. / Cui, H. / Jedrzejczak, R. / Edwards, A. / Savchenko, A. / Mabbutt, B.C. / Joachimiak, A.
History
DepositionJun 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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 / 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.db_align_beg / _struct_ref_seq.db_align_end / _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: ASCH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7632
Polymers18,7271
Non-polymers351
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.855, 39.689, 128.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein ASCH domain


Mass: 18727.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae TMA 21 (bacteria) / Gene: VCB_002424 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, 0.2 M MgCl2, 25% Peg 3350, 1/10 V8 paraton-N, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 9, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. all: 41267 / Num. obs: 38568 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.7 / % possible all: 78

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXmodel building
ARP/wARPmodel building
MOLREPphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→40 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.612 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.053 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17237 1937 5 %RANDOM
Rwork0.1342 ---
all0.14 38376 --
obs0.13612 36439 92.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.817 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 1 349 1645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221354
X-RAY DIFFRACTIONr_bond_other_d0.0030.02906
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.9291838
X-RAY DIFFRACTIONr_angle_other_deg1.11932203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85924.65873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2215231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.467156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021542
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02296
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_it2.3851.5804
X-RAY DIFFRACTIONr_mcbond_other0.8881.5328
X-RAY DIFFRACTIONr_mcangle_it3.37421293
X-RAY DIFFRACTIONr_scbond_it5.4163550
X-RAY DIFFRACTIONr_scangle_it7.7194.5540
X-RAY DIFFRACTIONr_rigid_bond_restr2.24332260
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 128 -
Rwork0.284 2247 -
obs--79.09 %

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