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- PDB-3cia: Crystal structure of cold-aminopeptidase from Colwellia psychrery... -

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Basic information

Entry
Database: PDB / ID: 3cia
TitleCrystal structure of cold-aminopeptidase from Colwellia psychrerythraea
Componentscold-active aminopeptidase
KeywordsHYDROLASE / PSYCHROHILIC
Function / homology
Function and homology information


membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / cytoplasm
Similarity search - Function
Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal domain / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain ...Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal domain / Peptidase M1, leukotriene A4 hydrolase/aminopeptidase C-terminal / Aminopeptidase, leukotriene A4 hydrolase-like / Peptidase M1, LTA-4 hydrolase/aminopeptidase, C-terminal domain superfamily / : / Leukotriene A4 hydrolase, C-terminal / Leukotriene A4 hydrolase, C-terminal / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBauvois, C. / Jacquamet, L. / Borel, F. / Ferrer, J.-L.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of the Cold-active Aminopeptidase from Colwellia psychrerythraea, a Close Structural Homologue of the Human Bifunctional Leukotriene A4 Hydrolase.
Authors: Bauvois, C. / Jacquamet, L. / Huston, A.L. / Borel, F. / Feller, G. / Ferrer, J.L.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: cold-active aminopeptidase
B: cold-active aminopeptidase
C: cold-active aminopeptidase
D: cold-active aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,9358
Polymers274,6734
Non-polymers2624
Water16,556919
1
A: cold-active aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7342
Polymers68,6681
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cold-active aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7342
Polymers68,6681
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: cold-active aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7342
Polymers68,6681
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: cold-active aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7342
Polymers68,6681
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.370, 87.100, 116.360
Angle α, β, γ (deg.)88.83, 70.68, 88.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
cold-active aminopeptidase / E.C.3.4.11.- / Neutral zinc metallopeptidase / M1 family


Mass: 68668.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / Gene: CPS_3470 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7WVY1, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 23 % w/v PEG 3350, 0.5 M NaCl, 0.1 M Bis-Tris, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799 Å
DetectorDetector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.7→46.7 Å / Num. all: 80533 / Num. obs: 74827 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.29 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.2 / Rsym value: 0.09 / Net I/σ(I): 8.57
Reflection shellResolution: 2.7→2.8 Å / % possible all: 67.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.2refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HS6

1hs6


Resolution: 2.7→46.68 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.84 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27011 4034 5 %RANDOM
Rwork0.24943 ---
obs0.25047 76497 97.29 %-
all-80533 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.193 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0.08 Å20.05 Å2
2---0.29 Å20.15 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18685 0 4 919 19608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02219141
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2281.94926017
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55352319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.03224.747929
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.562153184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7151584
X-RAY DIFFRACTIONr_chiral_restr0.1680.22852
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214651
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3140.210848
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3460.213274
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.21024
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.40.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1721.511623
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.097218718
X-RAY DIFFRACTIONr_scbond_it1.54437518
X-RAY DIFFRACTIONr_scangle_it2.3854.57299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 315 -
Rwork0.374 5632 -
obs--97.16 %

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