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- PDB-2bww: His350Ala Escherichia coli Aminopeptidase P -

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Basic information

Entry
Database: PDB / ID: 2bww
TitleHis350Ala Escherichia coli Aminopeptidase P
ComponentsAMINOPEPTIDASE P
KeywordsHYDROLASE / AMINOPEPTIDASE P / 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 ...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 / : / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2018Group: Advisory / Data collection / Database references / Category: citation / pdbx_unobs_or_zero_occ_atoms / Item: _citation.page_last
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry

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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)50,1186
Polymers49,6771
Non-polymers4415
Water2,738152
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)200,47424
Polymers198,7084
Non-polymers1,76620
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)138.170, 138.170, 231.296
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-2030-

HOH

21A-2032-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 49676.996 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/H350A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase

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Non-polymers , 5 types, 157 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


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


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 350 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: 5.6 Å3/Da / Density % sol: 77.7 % / Description: STARTING MODEL WAS STRIPPED OF HETATMS.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: SITTING DROP VAPOUR DIFFUSION AT 4C. 2 UL 7 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM ...Details: SITTING DROP VAPOUR DIFFUSION AT 4C. 2 UL 7 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM MNCL2 FOR 30 MIN 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: Jun 6, 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: 2.6→74.54 Å / Num. obs: 33663 / % possible obs: 97.2 % / Observed criterion σ(I): 6 / Redundancy: 5.4 % / Biso Wilson estimate: 58.02 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BHC

2bhc


Resolution: 2.61→69.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.361 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PEPTIDE BOND BETWEEN RESIDUES 88 AND 89 IS COMPLETELY DISORDERED AND COULD NOT BE MODELLED. INSUFFICIENT DENSITY WAS PRESENT FOR COMPLETE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PEPTIDE BOND BETWEEN RESIDUES 88 AND 89 IS COMPLETELY DISORDERED AND COULD NOT BE MODELLED. INSUFFICIENT DENSITY WAS PRESENT FOR COMPLETE MODELLING OF RESIDUES 439 AND 440
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1630 4.8 %RANDOM
Rwork0.172 ---
obs0.174 32029 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2--1.33 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.61→69.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 24 152 3660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223602
X-RAY DIFFRACTIONr_bond_other_d0.0010.023287
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9634886
X-RAY DIFFRACTIONr_angle_other_deg0.75437591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00423.37184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80515609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6611536
X-RAY DIFFRACTIONr_chiral_restr0.0650.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
X-RAY DIFFRACTIONr_nbd_refined0.2070.2738
X-RAY DIFFRACTIONr_nbd_other0.170.23367
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21740
X-RAY DIFFRACTIONr_nbtor_other0.080.22221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.75622359
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14733526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6641539
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.66261357
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: 2.61→2.68 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 128
Rwork0.295 2219
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)
11.2566-0.7385-0.33662.71650.55871.0101-0.0355-0.3685-0.04570.46910.1234-0.00380.00710.1299-0.0879-0.0041-0.0847-0.00850.0359-0.0353-0.077120.058771.403869.4043
20.8127-0.0205-0.12861.65690.52941.0380.04310.0140.1484-0.22040.034-0.2024-0.08140.2258-0.0772-0.09-0.05170.0228-0.0489-0.0344-0.121235.888553.122141.0263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 172
2X-RAY DIFFRACTION2A173 - 440

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