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- PDB-4fkc: Recombinant prolidase from Thermococcus sibiricus -

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Basic information

Entry
Database: PDB / ID: 4fkc
TitleRecombinant prolidase from Thermococcus sibiricus
ComponentsXaa-Pro aminopeptidase
KeywordsHYDROLASE / Pita-bread structure / Prolidase
Function / homology
Function and homology information


aminopeptidase activity / metal ion binding
Similarity search - Function
Creatinase, N-terminal / Creatinase/Prolidase 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 / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 ...Creatinase, N-terminal / Creatinase/Prolidase 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 / 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 speciesThermococcus sibiricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTrofimov, A.A. / Slutskaya, E.S. / Polyakov, K.M. / Dorovatovskii, P.V. / Gumerov, V.M. / Popov, V.O.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus.
Authors: Trofimov, A.A. / Slutskaya, E.A. / Polyakov, K.M. / Dorovatovskii, P.V. / Gumerov, V.M. / Popov, V.O.
History
DepositionJun 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / 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.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.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_symmetry / _struct_ref_seq_dif.details / _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)43,94813
Polymers42,5991
Non-polymers1,34912
Water95553
1
A: Xaa-Pro aminopeptidase
hetero molecules

A: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,89526
Polymers85,1972
Non-polymers2,69824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4700 Å2
ΔGint-150 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.700, 89.700, 165.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Xaa-Pro aminopeptidase /


Mass: 42598.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sibiricus (archaea) / Strain: MM 739 / DSM 12597 / Gene: TSIB_0821 / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami (DE3) / References: UniProt: C6A2N7
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Protein solution (2mcl): 10.8 mg/mL Tsprol and 150 mM NaCl in 50 mM Tris buffer (pH 7.6). Reservoir solution (2mcl): 100 mM CdCl2 and 30 % v/v PEG400 in 100 mM sodium acetate buffer (pH 4.6) ...Details: Protein solution (2mcl): 10.8 mg/mL Tsprol and 150 mM NaCl in 50 mM Tris buffer (pH 7.6). Reservoir solution (2mcl): 100 mM CdCl2 and 30 % v/v PEG400 in 100 mM sodium acetate buffer (pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.9887 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 11, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9887 Å / Relative weight: 1
ReflectionResolution: 2.6→78.83 Å / Num. all: 21480 / Num. obs: 21360 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.089 / Net I/σ(I): 24.5
Reflection shellResolution: 2.6→2.8 Å / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 4.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
AUTOMARdata collection
BALBESphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HOW

2how


Resolution: 2.6→78.83 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.895 / SU B: 10.042 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26859 1092 5.1 %RANDOM
Rwork0.231 ---
obs0.23293 20268 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→78.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 12 53 2916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222935
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9653954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0724.091132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52515471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1661515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212247
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6831.51834
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27622941
X-RAY DIFFRACTIONr_scbond_it1.79931101
X-RAY DIFFRACTIONr_scangle_it2.914.51013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 68 -
Rwork0.344 1476 -
obs--99.74 %

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