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- PDB-2o14: X-Ray Crystal Structure of Protein YXIM_BACsu from Bacillus subti... -

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Basic information

Entry
Database: PDB / ID: 2o14
TitleX-Ray Crystal Structure of Protein YXIM_BACsu from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR595
ComponentsHypothetical protein yxiM
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / SR595 / YXIM / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


carboxylic ester hydrolase activity / cell outer membrane / Hydrolases; Acting on ester bonds
Similarity search - Function
Rhamnogalacturonan acetylesterase RhgT-like / Galactose-binding lectin / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Rossmann fold ...Rhamnogalacturonan acetylesterase RhgT-like / Galactose-binding lectin / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Uncharacterized esterase YxiM
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsKuzin, A.P. / Chen, Y. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Chen, C.X. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of the hypothetical protein YXIM_BACsu from Bacillus subtilis.
Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Chen, C. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Hypothetical protein yxiM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7873
Polymers41,6361
Non-polymers1512
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.425, 59.774, 92.388
Angle α, β, γ (deg.)90.00, 100.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical protein yxiM


Mass: 41636.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: BL21(DE3)+Magic / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P42304
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: MnSo4.H2O 0.1M, MOPS 0.1M, PEG8000 20% (w/v), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908, 0.97932, 0.96797
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Oct 5, 2006 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979081
20.979321
30.967971
ReflectionResolution: 2.1→30 Å / Num. obs: 47440 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3738 / % possible all: 72

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.82 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 148992.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2122 4.9 %RANDOM
Rwork0.189 ---
obs0.189 43072 82.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5327 Å2 / ksol: 0.301931 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.75 Å20 Å2-7.91 Å2
2--1.67 Å20 Å2
3----6.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 6 268 2999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 234 5 %
Rwork0.22 4492 -
obs--54.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION4ion.paramion.top

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