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- PDB-2bhc: Na substituted E. coli Aminopeptidase P -

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Basic information

Entry
Database: PDB / ID: 2bhc
TitleNa substituted E. coli Aminopeptidase P
ComponentsXAA-PRO AMINOPEPTIDASE
KeywordsHYDROLASE / PROLINE-SPECIFIC PEPTIDASE / 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 / 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.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: An Orthorhombic Form of Escherichia Coli Aminopeptidase P at 2.4 Ang Resolution
Authors: Graham, S.C. / Lee, M. / Freeman, H.C. / Guss, J.M.
History
DepositionJan 10, 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 1.2Oct 22, 2014Group: Database references
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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)49,9804
Polymers49,7441
Non-polymers2363
Water2,684149
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)199,92216
Polymers198,9764
Non-polymers94612
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)138.783, 138.783, 231.012
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-2033-

HOH

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Components

#1: Protein XAA-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P / X-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P II / APP-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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHAS A CATALYTIC ACTIVITY

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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: 77.9 %
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 VAPOR DIFFUSION AT 4C. RESERVOIR CONTAINED 26% MPD, 100 MM NA.CITRATE (PH 7.5) AND 200 MM MG.ACETATE.

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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 28, 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: 43830 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 53.01 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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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: 0.953 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.147 / 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
Rfree0.202 2132 4.9 %RANDOM
Rwork0.176 ---
obs0.177 41640 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å20 Å2
2--1.42 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→60.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 15 149 3651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223598
X-RAY DIFFRACTIONr_bond_other_d0.0010.023273
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.964881
X-RAY DIFFRACTIONr_angle_other_deg0.76437562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1435439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99323.351185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02415610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0161536
X-RAY DIFFRACTIONr_chiral_restr0.0620.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
X-RAY DIFFRACTIONr_nbd_refined0.1980.2694
X-RAY DIFFRACTIONr_nbd_other0.1690.23259
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21715
X-RAY DIFFRACTIONr_nbtor_other0.080.22090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.85722185
X-RAY DIFFRACTIONr_mcbond_other0.22900
X-RAY DIFFRACTIONr_mcangle_it1.58933524
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.63441451
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.34961357
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% reflection
Rfree0.313 138 -
Rwork0.275 3065 -
obs--99.75 %
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)
10.806-0.5256-0.23791.5863-0.05280.91480.0252-0.21970.02740.23520.0502-0.0082-0.03880.0439-0.0754-0.0339-0.0978-0.0049-0.0237-0.0558-0.067120.14471.64869.246
20.5425-0.0831-0.08951.25380.33380.93020.03090.0010.0991-0.15080.0438-0.1774-0.00340.1632-0.0747-0.052-0.04160.0203-0.0112-0.0319-0.080135.54453.20441.006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 172
2X-RAY DIFFRACTION2A173 - 440

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