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- PDB-1vhe: Crystal structure of a aminopeptidase/glucanase homolog -

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Basic information

Entry
Database: PDB / ID: 1vhe
TitleCrystal structure of a aminopeptidase/glucanase homolog
Componentsaminopeptidase/glucanase homolog
KeywordsStructural genomics / unknown function
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / Peptidase M42, domain 2 / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative aminopeptidase YsdC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 1.9 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_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: aminopeptidase/glucanase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2532
Polymers41,1881
Non-polymers651
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: aminopeptidase/glucanase homolog
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)495,04124
Polymers494,25712
Non-polymers78512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
crystal symmetry operation30_555z,-x+1/2,-y+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation51_555-x+1/2,y,-z+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation74_555-x+1/2,-y+1/2,z1
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation84_555-y+1/2,-z+1/2,x1
Buried area61720 Å2
ΔGint-675 kcal/mol
Surface area132940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)223.966, 223.966, 223.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

21A-611-

HOH

31A-660-

HOH

41A-664-

HOH

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Components

#1: Protein aminopeptidase/glucanase homolog


Mass: 41188.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ysdC / Production host: Escherichia coli (E. coli) / References: UniProt: P94521
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795, 0.9641
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.96411
ReflectionResolution: 1.9→45.72 Å / Num. all: 38362 / Num. obs: 38362 / % possible obs: 99.9 % / Redundancy: 41.84 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 34.7
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 13.1 / % possible all: 99.3
Reflection
*PLUS
Redundancy: 41.8 % / Rmerge(I) obs: 0.13
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC4refinement
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 1.9→45.72 Å / σ(F): 0
RfactorNum. reflection
Rfree0.193 1921
Rwork0.176 -
obs-38362
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 418.204 Å2 / ksol: 0.992 e/Å3
Displacement parametersBiso mean: 10.954 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.9→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 1 362 3127
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_d1.571
X-RAY DIFFRACTIONp_planar_tor1.547
X-RAY DIFFRACTIONp_chiral_restr0.109
X-RAY DIFFRACTIONp_plane_restr0.006
X-RAY DIFFRACTIONp_mcbond_it1.098
X-RAY DIFFRACTIONp_mcangle_it1.886
X-RAY DIFFRACTIONp_scbond_it2.388
X-RAY DIFFRACTIONp_scangle_it3.298
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6

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