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- PDB-2bwv: His361Ala Escherichia coli Aminopeptidase P -

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Basic information

Entry
Database: PDB / ID: 2bwv
TitleHis361Ala Escherichia coli Aminopeptidase P
ComponentsAMINOPEPTIDASE PXaa-Pro aminopeptidase
KeywordsHYDROLASE / METALLOENZYME / 'PITA-BREAD' ENZYME / PROLINE-SPECIFIC ENZYME / MANGANESE ENZYME
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 / Creatine Amidinohydrolase ...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
: / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGraham, S.C. / Guss, J.M.
CitationJournal: Biochemistry / Year: 2006
Title: Kinetic and Crystallographic Analysis of Mutant Escherichia Coli Aminopeptidase P: Insights Into Substrate Recognition and the Mechanism of Catalysis.
Authors: Graham, S.C. / Lilley, P.E. / Lee, M. / Schaeffer, P.M. / Kralicek, A.V. / Dixon, N.E. / Guss, J.M.
History
DepositionJul 19, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 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_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.ptnr2_auth_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMINOPEPTIDASE P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8384
Polymers49,6931
Non-polymers1453
Water11,692649
1
A: AMINOPEPTIDASE P
hetero molecules

A: AMINOPEPTIDASE P
hetero molecules

A: AMINOPEPTIDASE P
hetero molecules

A: AMINOPEPTIDASE P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,35316
Polymers198,7724
Non-polymers58112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area12400 Å2
ΔGint-20 kcal/mol
Surface area85590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.339, 177.339, 96.475
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein AMINOPEPTIDASE P / Xaa-Pro aminopeptidase / AMINOPEPTIDASE P / X-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P II / APP-II / AMINOACYLPROLINE AMINOPEPTIDASE


Mass: 49692.996 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: AN1459 / Plasmid: PPL670/H361A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 649 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 361 TO ALA

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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: 4.4 Å3/Da / Density % sol: 71.9 %
Description: STARTING MODEL WAS STRIPPED OF HETATMS AND MULTIPLE CONFORMERS
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 6 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28 % PEG 4K, 0.1 M TRIS PH 8.5. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10% MPD AND 1 MM MNCL2 ...Details: HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 6 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28 % PEG 4K, 0.1 M TRIS PH 8.5. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10% MPD AND 1 MM MNCL2 FOR 1 HR AT 4C PRIOR TO CRYOCOOLING.

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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: Apr 5, 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: 1.7→65.23 Å / Num. obs: 96986 / % possible obs: 99.4 % / Observed criterion σ(I): 6 / Redundancy: 6 % / Biso Wilson estimate: 22.44 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WL9

1wl9


Resolution: 1.7→154.3 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.188 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.165 2938 3 %RANDOM
Rwork0.15 ---
obs0.15 94042 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→154.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 3 649 4147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223628
X-RAY DIFFRACTIONr_bond_other_d0.0010.023303
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9564928
X-RAY DIFFRACTIONr_angle_other_deg0.80337662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9025457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82823.67188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.77215623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3141534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
X-RAY DIFFRACTIONr_nbd_refined0.210.2728
X-RAY DIFFRACTIONr_nbd_other0.1760.23406
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21737
X-RAY DIFFRACTIONr_nbtor_other0.0790.22044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2407
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.02722903
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.26533574
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.85741630
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.59461345
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 219
Rwork0.302 6851
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)
10.8904-0.06510.38040.6338-0.0750.5866-0.06350.02440.13830.0359-0.00180.0053-0.12970.0280.0653-0.07380.0217-0.0145-0.06980.0036-0.071160.967280.541448.4865
20.4113-0.16740.1110.5093-0.13951.03590.00940.0042-0.06290.0129-0.02210.06880.2075-0.02760.0127-0.07360.01550.0161-0.1091-0.0057-0.09767.359643.782350.6096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 172
2X-RAY DIFFRACTION2A173 - 440

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