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- PDB-3q69: X-ray crystal structure of a MucBP domain of the protein LBA1460 ... -

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Basic information

Entry
Database: PDB / ID: 3q69
TitleX-ray crystal structure of a MucBP domain of the protein LBA1460 from Lactobacillus acidophilus, Northeast structural genomics consortium target LaR80A
Componentsprobable Zn binding protein
KeywordsMETAL BINDING PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / domain family PF06458
Function / homologyImmunoglobulin-like - #4300 / Mub B2-like domain / Muc B2-like domain / Immunoglobulin-like / Sandwich / Mainly Beta / Putative mucus binding protein
Function and homology information
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSeetharaman, J. / Lew, S. / Forouhar, F. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. ...Seetharaman, J. / Lew, S. / Forouhar, F. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray crystal structure of a MucBP domain of the protein LBA1460 from Lactobacillus acidophilus, Northeast structural genomics consortium target LaR80A
Authors: Seetharaman, J. / Lew, S. / Forouhar, F. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionDec 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 6, 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

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Assembly

Deposited unit
A: probable Zn binding protein


Theoretical massNumber of molelcules
Total (without water)14,0931
Polymers14,0931
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.789, 24.855, 83.363
Angle α, β, γ (deg.)90.00, 108.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein probable Zn binding protein / Putative mucus binding protein


Mass: 14093.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: LBA1460 / References: UniProt: Q5FJ43
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, .1M KBr .1M Bis Tris Propane pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 11754 / Num. obs: 9462 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.063
Reflection shellResolution: 2.4→2.44 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.29 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 937353.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.292 835 9.3 %RANDOM
Rwork0.234 ---
obs0.234 8945 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.5739 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.87 Å20 Å21.05 Å2
2--13.81 Å20 Å2
3----7.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 0 63 903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.76
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 145 9.8 %
Rwork0.279 1328 -
obs--95.4 %
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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