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- PDB-2bn7: Mn substituted E. coli Aminopeptidase P in complex with product and Zn -

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Basic information

Entry
Database: PDB / ID: 2bn7
TitleMn substituted E. coli Aminopeptidase P in complex with product and Zn
ComponentsXAA-PRO AMINOPEPTIDASE
KeywordsHYDROLASE / PROLINE-SPECIFIC PEPTIDASE / PRODUCT COMPLEX / METALLOENZYME / PITA-BREAD FOLD / DINUCLEAR HYDROLASE
Function / homology
Function and homology information


Xaa-Pro aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / protein homotetramerization / protein-containing complex / proteolysis / identical protein binding / cytosol
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / : / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / : / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / LEUCINE / : / PROLINE / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGraham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.
CitationJournal: Biochemistry / Year: 2005
Title: Structural and Functional Implications of Metal Ion Selection in Aminopeptidase P, a Metalloprotease with a Dinuclear Metal Center.
Authors: Graham, S.C. / Bond, C.S. / Freeman, H.C. / Guss, J.M.
History
DepositionMar 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _citation.page_last / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._citation.page_last / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _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: XAA-PRO AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3798
Polymers49,7441
Non-polymers6357
Water5,152286
1
A: XAA-PRO AMINOPEPTIDASE
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,51632
Polymers198,9764
Non-polymers2,54028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)139.695, 139.695, 230.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2065-

HOH

21A-2069-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein XAA-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P / X-PRO AMINOPEPTIDASE / AMINO- PEPTIDASE P II / APP-II / AMINOACYLPROLINE AMINOPEPTIDASE


Mass: 49744.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DIPEPTIDE PRODUCT OF AMINOPEPTIDASE P (FORMED BY CLEVAGE OF XAA-PRO-LEU TRIPEPTIDE SUBSTRATE)
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: AN1459 / Plasmid: PPL670 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase

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Non-polymers , 7 types, 293 molecules

#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 5.25 Å3/Da / Density % sol: 76.4 %
Crystal growTemperature: 277 K / pH: 7.5
Details: AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN IN 22% MPD, 100 MM NACITRATE (PH 7.5) AND 200 MM MGACETATE AT 4C. CRYSTALS WERE SOAKED FOR 1 HOUR IN ...Details: AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN IN 22% MPD, 100 MM NACITRATE (PH 7.5) AND 200 MM MGACETATE AT 4C. CRYSTALS WERE SOAKED FOR 1 HOUR IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM MNCL2, 1 MM ZNCL2 AND 10 MM PROLEU DIPEPTIDE PRIOR TO DATA COLLECTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→60 Å / Num. obs: 44853 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 55.06 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N51 STRIPPED OF MULTIPLE CONFORMERS, SOLVENT ATOMS AND HETERO COMPOUNDS

1n51


Resolution: 2.4→119.52 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 7.752 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INSUFFICIENT DENSITY WAS PRESENT TO ALLOW COMPLETE MODELLING OF C-TERMINAL RESIDUES 439 AND 440.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2184 4.9 %RANDOM
Rwork0.165 ---
obs0.166 42588 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å20 Å2
2--1.41 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.4→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 33 286 3806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223613
X-RAY DIFFRACTIONr_bond_other_d0.0010.023285
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.9614903
X-RAY DIFFRACTIONr_angle_other_deg0.75437593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90923.459185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4715610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0281535
X-RAY DIFFRACTIONr_chiral_restr0.0590.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
X-RAY DIFFRACTIONr_nbd_refined0.1880.2693
X-RAY DIFFRACTIONr_nbd_other0.1690.23300
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21718
X-RAY DIFFRACTIONr_nbtor_other0.080.22097
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.82922382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21133544
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.00541535
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.10161355
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.33 138
Rwork0.284 3095
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8848-0.5348-0.251.92690.0671.05640.0064-0.28980.07610.2730.0939-0.057-0.02120.0944-0.1002-0.0728-0.0929-0.0043-0.0274-0.0692-0.117520.125472.02769.1679
20.7021-0.038-0.12841.46910.41281.22720.03060.02740.1274-0.17450.0559-0.1788-0.01380.1598-0.0865-0.1354-0.03770.0221-0.0729-0.0315-0.167435.662953.72240.6916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 172
2X-RAY DIFFRACTION2A173 - 440

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