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- PDB-1hi9: Zn-dependent D-aminopeptidase DppA from Bacillus subtilis, a self... -

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Basic information

Entry
Database: PDB / ID: 1hi9
TitleZn-dependent D-aminopeptidase DppA from Bacillus subtilis, a self-compartmentalizing protease.
ComponentsDIPEPTIDE TRANSPORT PROTEIN DPPA
KeywordsHYDROLASE (PROTEASE) / PROTEASE / D-AMINOPEPTIDASE / DECAMER / SELF-COMPARTMENTALIZING
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / sporulation resulting in formation of a cellular spore / aminopeptidase activity / metallopeptidase activity / metal ion binding
Similarity search - Function
Dipeptide transport protein / Dipeptide transport protein / Peptidase M55, D-aminopeptidase / D-aminopeptidase, N-terminal / D-aminopeptidase DppA / Peptidase M55, D-aminopeptidase superfamily / D-aminopeptidase / Gyrase A; domain 2 / Rossmann fold / 2-Layer Sandwich ...Dipeptide transport protein / Dipeptide transport protein / Peptidase M55, D-aminopeptidase / D-aminopeptidase, N-terminal / D-aminopeptidase DppA / Peptidase M55, D-aminopeptidase superfamily / D-aminopeptidase / Gyrase A; domain 2 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsRemaut, H. / Bompard-Gilles, C. / Goffin, C. / Frere, J.M. / Van Beeumen, J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of the Bacillus Subtilis D-Aminopeptidase Dppa Reveals a Novel Self-Compartmentalizing Protease
Authors: Remaut, H. / Bompard-Gilles, C. / Goffin, C. / Frere, J.M. / Van Beeumen, J.
History
DepositionJan 4, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPEPTIDE TRANSPORT PROTEIN DPPA
B: DIPEPTIDE TRANSPORT PROTEIN DPPA
C: DIPEPTIDE TRANSPORT PROTEIN DPPA
D: DIPEPTIDE TRANSPORT PROTEIN DPPA
E: DIPEPTIDE TRANSPORT PROTEIN DPPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,03715
Polymers151,3835
Non-polymers65410
Water4,450247
1
A: DIPEPTIDE TRANSPORT PROTEIN DPPA
B: DIPEPTIDE TRANSPORT PROTEIN DPPA
C: DIPEPTIDE TRANSPORT PROTEIN DPPA
D: DIPEPTIDE TRANSPORT PROTEIN DPPA
E: DIPEPTIDE TRANSPORT PROTEIN DPPA
hetero molecules

A: DIPEPTIDE TRANSPORT PROTEIN DPPA
B: DIPEPTIDE TRANSPORT PROTEIN DPPA
C: DIPEPTIDE TRANSPORT PROTEIN DPPA
D: DIPEPTIDE TRANSPORT PROTEIN DPPA
E: DIPEPTIDE TRANSPORT PROTEIN DPPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,07530
Polymers302,76710
Non-polymers1,30820
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)145.110, 165.860, 109.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.61104, -0.70926, -0.35155), (0.7144, 0.30279, 0.63083), (-0.34097, -0.63661, 0.69171)66.89993, -40.49408, 59.21963
2given(-0.00624, -0.44029, -0.89784), (0.43558, -0.8094, 0.39389), (-0.90013, -0.38862, 0.19684)115.9103, 31.78131, 103.19849
3given(-0.02074, 0.44752, -0.89403), (-0.44105, -0.8066, -0.39353), (-0.89724, 0.38615, 0.21411)80.21922, 116.98578, 70.84882
4given(0.61609, 0.71465, -0.33123), (-0.70737, 0.317, -0.63177), (-0.3465, 0.62353, 0.70082)7.87976, 96.86948, 7.79661
DetailsTHE ENZYME IS A HOMODECAMER WITH 52 POINT -GROUP SYMMETRY

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Components

#1: Protein
DIPEPTIDE TRANSPORT PROTEIN DPPA / DCIAA


Mass: 30276.670 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Description: RECOMBINANT EXPRESSION IN E. COLI / Cellular location: CYTOPLASM / Gene: DCIAA / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P26902
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.16 Å3/Da / Density % sol: 43 % / Description: ANOMALOUS SCATERRERS: 2 ZN2+/274AA.
Crystal growpH: 8.5
Details: 18% PEG6000, 100MM TRIS, PH 8.5, 5MM NACL, 5MM MGCL2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
210 mMTris1drop
35 mM1dropNaN3
418 %(w/v)PEG60001reservoir
5100 mMTris1reservoir
65 mM1reservoirNaCl
75 mM1reservoirMgCl2
85 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8445,1.2832,1.2834
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.84451
21.28321
31.28341
ReflectionResolution: 2.403→20 Å / Num. obs: 51831 / % possible obs: 96.9 % / Redundancy: 3.48 % / Biso Wilson estimate: 48.6 Å2 / Rsym value: 0.055 / Net I/σ(I): 11.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.247 / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 438502 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.247

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→15 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: INITIAL REFINEMENT WITH REFMAC DURING MODEL BUILDING
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2544 5 %RANDOM
Rwork0.232 ---
obs0.232 49995 96.8 %-
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-11.275 Å20 Å20 Å2
2---11.094 Å20 Å2
3----0.182 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10570 0 10 247 10827
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.24
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_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.652.5
Refine LS restraints NCSNCS model details: RESTRAINTS

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