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- PDB-2bha: E. coli Aminopeptidase P in complex with substrate -

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Basic information

Entry
Database: PDB / ID: 2bha
TitleE. coli Aminopeptidase P in complex with substrate
Components
  • VALINE-PROLINE-LEUCINE
  • XAA-PRO AMINOPEPTIDASE
KeywordsHYDROLASE / HYDROLASE-SUBSTRATE COMPLEX / PROLINE-SPECIFIC PEPTIDASE / SUBSTRATE 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 / 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
CITRATE ANION / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
SYNTHETIC CONSTRUCT (others)
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
DepositionJan 8, 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 1.2Feb 8, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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: XAA-PRO AMINOPEPTIDASE
B: VALINE-PROLINE-LEUCINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2854
Polymers50,0712
Non-polymers2132
Water1,964109
1
A: XAA-PRO AMINOPEPTIDASE
B: VALINE-PROLINE-LEUCINE
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)201,14016
Polymers200,2868
Non-polymers8548
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
Buried area6350 Å2
ΔGint-18.5 kcal/mol
Surface area35260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.223, 138.223, 230.841
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-2018-

HOH

DetailsAMINOPEPTIDASE P IS A HOMOTETRAMER IN SOLUTION. HOWEVER, SINCE IN THIS ENTRY, EACH CHAIN OF THIS PROTEIN IS INCOMPLEX WITH A TRIPEPTIDE, THIS ENTRY IS CLASSIFIEDAS A HETEROOCTAMER.

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Components

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


Mass: 49744.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
#2: Protein/peptide VALINE-PROLINE-LEUCINE


Mass: 327.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TRIPEPTIDE SUBSTRATE OF AMINOPEPTIDASE P / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#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 / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 5.5 Å3/Da / Density % sol: 77.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN USING HANGING DROP VAOPR DIFFUSION AT 4C. RESERVOIR CONTAINED 26% MPD, 100 MM NA.CITRATE (PH 7.5) AND ...Details: AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN USING HANGING DROP VAOPR DIFFUSION AT 4C. RESERVOIR CONTAINED 26% MPD, 100 MM NA.CITRATE (PH 7.5) AND 200 MM MG.ACETATE. CRYSTALS WERE SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10 MM VALPROLEU TRIPEPTIDE FOR 1 HOUR AT 4C 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: Oct 26, 2004 / 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: 43763 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 52.55 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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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→60.19 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.603 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SUFFICIENT DENSITY WAS NOT PRESENT TO ALLOW FOR COMPLETE MODELLING OF RESIDUES A439 OR A440
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2130 4.9 %RANDOM
Rwork0.177 ---
obs0.178 41583 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--1.54 Å20 Å2
3----3.09 Å2
Refinement stepCycle: LAST / Resolution: 2.4→60.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 14 109 3633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223628
X-RAY DIFFRACTIONr_bond_other_d0.0010.023313
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.9624922
X-RAY DIFFRACTIONr_angle_other_deg0.76937653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03223.28186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40515616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4231537
X-RAY DIFFRACTIONr_chiral_restr0.0660.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02765
X-RAY DIFFRACTIONr_nbd_refined0.1910.2668
X-RAY DIFFRACTIONr_nbd_other0.1680.23271
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21704
X-RAY DIFFRACTIONr_nbtor_other0.080.22104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1722418
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61333554
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.60741551
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.98261365
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
Rfree0.337 140
Rwork0.266 3030
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)
10.8312-0.2371-0.18622.0301-0.09240.87580.033-0.2370.04760.26760.0384-0.0478-0.04450.0596-0.0714-0.0488-0.0987-0.0025-0.0212-0.0665-0.096119.977671.318269.3217
20.6298-0.1377-0.13881.43970.40391.08010.04430.00740.1092-0.16630.0354-0.1969-0.0070.1667-0.0797-0.0561-0.05340.0253-0.0151-0.0305-0.088435.825353.202940.9429
330.8569-12.279117.1238.177225.103240.09630.7348-1.2708-0.0952-1.56580.68090.9061-0.36860.7309-1.41580.021-0.04040.03990.0184-0.04970.024727.956258.589343.0057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 172
2X-RAY DIFFRACTION2A173 - 440
3X-RAY DIFFRACTION3B0 - 2

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