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- PDB-1xoc: The structure of the oligopeptide-binding protein, AppA, from Bac... -

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Basic information

Entry
Database: PDB / ID: 1xoc
TitleThe structure of the oligopeptide-binding protein, AppA, from Bacillus subtilis in complex with a nonapeptide.
Components
  • Nonapeptide VDSKNTSSW
  • Oligopeptide-binding protein appA
KeywordsTRANSPORT PROTEIN / oligopeptide / AppA / transport / Bacillus subtilis
Function / homology
Function and homology information


establishment of competence for transformation / peptide transport / peptide transmembrane transporter activity / sporulation resulting in formation of a cellular spore / ATP-binding cassette (ABC) transporter complex / protein transport / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Oligopeptide-binding protein AppA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MIR / Resolution: 1.55 Å
AuthorsLevdikov, V.M. / Blagova, E.V. / Brannigan, J.A. / Wright, L. / Vagin, A.A. / Wilkinson, A.J.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: The structure of the oligopeptide-binding protein, AppA, from Bacillus subtilis in complex with a nonapeptide.
Authors: Levdikov, V.M. / Blagova, E.V. / Brannigan, J.A. / Wright, L. / Vagin, A.A. / Wilkinson, A.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of the oligopeptide-binding protein AppA from Bacillus subtilis.
Authors: Wright, L. / Blagova, E. / Levdikov, V.M. / Brannigan, J.A. / Pattenden, R.J. / Chambers, J. / Wilkinson, A.J.
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 10, 2014Group: Database references
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: Oligopeptide-binding protein appA
B: Nonapeptide VDSKNTSSW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,40617
Polymers60,4252
Non-polymers98115
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-305 kcal/mol
Surface area20280 Å2
MethodPISA
2
A: Oligopeptide-binding protein appA
B: Nonapeptide VDSKNTSSW
hetero molecules

A: Oligopeptide-binding protein appA
B: Nonapeptide VDSKNTSSW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,81234
Polymers120,8504
Non-polymers1,96230
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6560 Å2
ΔGint-716 kcal/mol
Surface area40160 Å2
MethodPISA
3
A: Oligopeptide-binding protein appA
B: Nonapeptide VDSKNTSSW
hetero molecules

A: Oligopeptide-binding protein appA
B: Nonapeptide VDSKNTSSW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,81234
Polymers120,8504
Non-polymers1,96230
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7010 Å2
ΔGint-708 kcal/mol
Surface area39700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.955, 90.779, 54.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Oligopeptide-binding protein appA / Oligopeptide ABC transporter


Mass: 59400.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: appA / Plasmid: pMALP2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P42061
#2: Protein/peptide Nonapeptide VDSKNTSSW


Mass: 1024.063 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.6 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, zinc acetate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 18, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 88121 / Num. obs: 88121 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.5
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.788 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6467 / % possible all: 72.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, MIR
Starting model: pdb entry 1DPE

1dpe


Resolution: 1.55→30.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.343 / SU ML: 0.061 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20593 4411 5 %RANDOM
Rwork0.17552 ---
all0.17703 83608 --
obs0.17703 83608 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.752 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 15 441 4620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224289
X-RAY DIFFRACTIONr_bond_other_d0.0010.023749
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9635793
X-RAY DIFFRACTIONr_angle_other_deg1.1238857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50825.981209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87515796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.466158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.2160.2887
X-RAY DIFFRACTIONr_nbd_other0.1770.23813
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22118
X-RAY DIFFRACTIONr_nbtor_other0.0860.22403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2370
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.215
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1490.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0481.53340
X-RAY DIFFRACTIONr_mcbond_other0.2181.51039
X-RAY DIFFRACTIONr_mcangle_it1.2624138
X-RAY DIFFRACTIONr_scbond_it2.45232126
X-RAY DIFFRACTIONr_scangle_it3.4624.51655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 274 -
Rwork0.289 5562 -
obs-4411 100 %

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