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- PDB-3hnm: Crystal Structure of Protein BT_411 (putative chitobiase, fragmen... -

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Basic information

Entry
Database: PDB / ID: 3hnm
TitleCrystal Structure of Protein BT_411 (putative chitobiase, fragment 298-461) from Bacteroides thetaiotaomicron, Northeast Structural Genomics Consortium Target BtR319D
ComponentsPutative chitobiase
KeywordsStructural Genomics / unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / BtR319D.BT_411
Function / homology
Function and homology information


Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsKuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Nair, R. ...Kuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Northeast Structural Genomics Consortium Target BtR319D
Authors: Kuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative chitobiase
B: Putative chitobiase
C: Putative chitobiase
D: Putative chitobiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9738
Polymers79,8764
Non-polymers974
Water00
1
A: Putative chitobiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9932
Polymers19,9691
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative chitobiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9932
Polymers19,9691
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative chitobiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9932
Polymers19,9691
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative chitobiase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9932
Polymers19,9691
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.520, 141.520, 232.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein
Putative chitobiase


Mass: 19968.914 Da / Num. of mol.: 4 / Fragment: sequence database residues 298-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_0441 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8AAM3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growpH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97909, 0.97922, 0.96790
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2009 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979091
20.979221
30.96791
ReflectionResolution: 3→50 Å / Num. obs: 90200 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.101 / Rsym value: 0.423 / Net I/σ(I): 15.7

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
Auto-Rickshawphasing
SnBphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 3→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.2808 7664 8.5 %
Rwork0.2347 --
obs-45070 86.9 %
Solvent computationBsol: 5.72 Å2
Displacement parametersBiso mean: 46.15 Å2
Baniso -1Baniso -2Baniso -3
1--11.899 Å20 Å20 Å2
2---11.899 Å20 Å2
3---23.798 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5444 0 4 0 5448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.71
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2951.5
X-RAY DIFFRACTIONc_mcangle_it2.2692
X-RAY DIFFRACTIONc_scbond_it1.6092
X-RAY DIFFRACTIONc_scangle_it2.5932.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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