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- PDB-2v3y: His361Ala Escherichia coli aminopeptidase P in complex with product -

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Basic information

Entry
Database: PDB / ID: 2v3y
TitleHis361Ala Escherichia coli aminopeptidase P in complex with product
Components
  • TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
  • XAA-PRO AMINOPEPTIDASE
KeywordsHYDROLASE / 'PITA-BREAD' ENZYME / PROLINE- SPECIFIC ENZYME / AMINOPEPTIDASE P / MANGANESE ENZYME / PROTEASE / MANGANESE / METAL-BINDING / METALLOENZYME / AMINOPEPTIDASE / METALLOPROTEASE
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
: / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGraham, S.C. / Guss, J.M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2008
Title: Complexes of Mutants of Escherichia Coli Aminopeptidase P and the Tripeptide Substrate Valproleu.
Authors: Graham, S.C. / Guss, J.M.
History
DepositionJun 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 25, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 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
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.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
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1665
Polymers50,0202
Non-polymers1453
Water13,187732
1
A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules

A: XAA-PRO AMINOPEPTIDASE
B: TRIPEPTIDE (VALINE-PROLINE-LEUCINE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,66320
Polymers200,0828
Non-polymers58112
Water1448
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 area26550 Å2
ΔGint-27.8 kcal/mol
Surface area85130 Å2
MethodPQS
Unit cell
Length a, b, c (Å)177.132, 177.132, 96.170
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 XAA-PRO AMINOPEPTIDASE / X-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P II / APP-II / AMINOACYLPROLINE AMINOPEPTIDASE / AMINOPEPTIDASE P


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) / Plasmid: PPL670 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase
#2: Protein/peptide TRIPEPTIDE (VALINE-PROLINE-LEUCINE)


Mass: 327.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TRIPEPTIDE SUBSTRATE OF AMINOPEPTIDASE P / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


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


Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 361 TO ALA
Has protein modificationY
Sequence detailsHIS361ALA MUTANT

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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: 72 %
Description: STARTING MODEL WAS STRIPPED OF LIGANDS, SOLVENT AND ALTERNATE CONFORMERS BEFORE REFINEMENT
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALLISED IN 26% PEG 4K, 0.1 M TRIS PH 8.5 AT 277K. SOAKED IN 26% PEG 4K, 0.1 M TRIS PH 8.5, 1 MM MNCL2, 5 MM VAL-PRO-LEU, 10% MPD FOR 60 MIN AT 277K IMMEDIATELY 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 4, 2005 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→65.1 Å / Num. obs: 116058 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 19.28 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WL9

1wl9


Resolution: 1.6→154.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.705 / SU ML: 0.032 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 3514 3 %RANDOM
Rwork0.154 ---
obs0.154 112528 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→154.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 3 732 4246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223773
X-RAY DIFFRACTIONr_bond_other_d0.0020.022606
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9585149
X-RAY DIFFRACTIONr_angle_other_deg0.90136331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6223.485198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29215659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2961539
X-RAY DIFFRACTIONr_chiral_restr0.0810.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02803
X-RAY DIFFRACTIONr_nbd_refined0.2160.2779
X-RAY DIFFRACTIONr_nbd_other0.1940.22887
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21828
X-RAY DIFFRACTIONr_nbtor_other0.0830.21912
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2458
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.260
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.02323026
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.27333722
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.70941697
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.26861404
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 236
Rwork0.32 8243
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)
10.5078-0.1093-0.06350.475-0.190.58290.02890.04880.03130.0033-0.0199-0.015-0.05180.0098-0.0090.03510.0188-0.00650.0638-0.0004-0.001764.97274.69447.604
21.75220.00860.6890.54730.04760.5634-0.1148-0.00720.18440.03580.0280.0301-0.12460.01590.08670.04820.0292-0.01580.03520.0030.002358.68785.14948.999
30.3523-0.12720.09590.3774-0.12850.78770.01130.0077-0.04940.006-0.01620.0520.1565-0.01260.00490.06630.01270.00750.0411-0.00390.001766.99544.35650.252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 66
2X-RAY DIFFRACTION2A67 - 166
3X-RAY DIFFRACTION3A167 - 440

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