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- PDB-1m35: Aminopeptidase P from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1m35
TitleAminopeptidase P from Escherichia coli
ComponentsAMINOPEPTIDASE PXaa-Pro aminopeptidase
KeywordsHYDROLASE / Aminopeptidase / proline specific / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGraham, S.C. / Lee, M. / Freeman, H.C. / Guss, J.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: An orthorhombic form of Escherichia coli aminopeptidase P at 2.4 A resolution.
Authors: Graham, S.C. / Lee, M. / Freeman, H.C. / Guss, J.M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli
Authors: Wilce, M.C.J. / Bond, C.S. / Dixon, N.E. / Freeman, H.C. / Guss, J.M. / Lilley, P.E. / Wilce, J.A.
History
DepositionJun 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_site
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.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
B: AMINOPEPTIDASE P
C: AMINOPEPTIDASE P
D: AMINOPEPTIDASE P
E: AMINOPEPTIDASE P
F: AMINOPEPTIDASE P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,12418
Polymers298,4646
Non-polymers65912
Water29,1481618
1
A: AMINOPEPTIDASE P
B: AMINOPEPTIDASE P
C: AMINOPEPTIDASE P
D: AMINOPEPTIDASE P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,41612
Polymers198,9764
Non-polymers4408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: AMINOPEPTIDASE P
F: AMINOPEPTIDASE P
hetero molecules

E: AMINOPEPTIDASE P
F: AMINOPEPTIDASE P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,41612
Polymers198,9764
Non-polymers4408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)209.047, 313.963, 162.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsBiological assembly is a tetramer formed by chains A,B,C and D / Biological assembly is a tetramer formed by chains E and F and the two-fold axis: x, -y, -z

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Components

#1: Protein
AMINOPEPTIDASE P / Xaa-Pro aminopeptidase / AMPP / Aminoacylproline aminopeptidase / X-Pro aminopeptidase


Mass: 49744.062 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pepP / Plasmid: pPL670 / 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.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1618 / 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: 4.58 Å3/Da / Density % sol: 72.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: PEG 4000, Tris.HCl, sodium acetate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
220 mMTris1droppH8.5
325 %PEG40001reservoir
40.1 MTris-HCl1reservoir
50.2 Msodium acetate1reservoirpH8.0
610 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 25, 2002
Details: 58 cm long, Pt-coated, fused silica, vertical focus mirror
RadiationMonochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 197708 / Num. obs: 197708 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.16 % / Biso Wilson estimate: 34.7 Å2 / Limit h max: 87 / Limit h min: 0 / Limit k max: 130 / Limit k min: 0 / Limit l max: 67 / Limit l min: 0 / Observed criterion F max: 5063737.88 / Observed criterion F min: 17 / Rsym value: 0.058 / Net I/σ(I): 22.67
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.83 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 18004 / Rsym value: 0.3 / % possible all: 87.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Lowest resolution: 2.51 Å / % possible obs: 87.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Tetramer of aminopeptidase P from Escherichia coli. Tetramer created from structure of hexagonal form (PDB code 1AZ9) using crystallographic symmetry

1az9
PDB Unreleased entry


Resolution: 2.4→19.99 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1
Isotropic thermal model: Unrestrained, grouped. ARG, LYS, GLU and GLN had 3 groups per residue.
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 9679 4.9 %Random
Rwork0.195 ---
all-206112 --
obs-197455 95.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 32.421 Å2 / ksol: 0.319566 e/Å3
Displacement parametersBiso max: 100.49 Å2 / Biso mean: 37.91 Å2 / Biso min: 7.75 Å2
Baniso -1Baniso -2Baniso -3
1--4.09 Å20 Å20 Å2
2---5.84 Å20 Å2
3---9.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.27 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20994 0 12 1618 22624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_torsion_deg22.2
X-RAY DIFFRACTIONc_torsion_impr_deg0.79
Refine LS restraints NCSNCS model details: restrained / Weight Biso : 2 / Weight position: 100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.490.2928844.90.263171850.01205271806988
2.49-2.580.2888774.80.253174550.01204971833289.4
2.58-2.70.2569164.90.241178700.008205281878691.5
2.7-2.840.2589174.70.232185230.009204841944094.9
2.84-3.020.251100850.227190620.008205382007097.7
3.02-3.250.2479904.80.23194570.008205702044799.4
3.25-3.580.2379814.80.216195150.008206012049699.5
3.58-4.090.21110024.90.187194760.007206582047899.1
4.09-5.140.159103250.139195240.005207572055699
5.14-19.990.16410725.20.152197090.005211652078198.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramwater.top
X-RAY DIFFRACTION3water_rep.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 2.51 Å

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