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- PDB-4rgz: Crystal structure of recombinant prolidase from Thermococcus sibi... -

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Basic information

Entry
Database: PDB / ID: 4rgz
TitleCrystal structure of recombinant prolidase from Thermococcus sibiricus at P21221 spacegroup
ComponentsXaa-Pro aminopeptidase
KeywordsHYDROLASE / Aminopeptidase / Dipeptidases
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 ...: / 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
PHOSPHATE ION / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesThermococcus sibiricus MM 739 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTimofeev, V.I. / Korgenevsky, D.A. / Gorbacheva, M.A. / Boyko, K.M. / Slutsky, E. / Rakitina, T.V. / Lipkin, A.V. / Popov, V.O.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of recombinant prolidase from Thermococcus sibiricus in space group P21221.
Authors: Timofeev, V. / Slutskaya, E. / Gorbacheva, M. / Boyko, K. / Rakitina, T. / Korzhenevskiy, D. / Lipkin, A. / Popov, V.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal_grow / 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 / _exptl_crystal_grow.method / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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_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
N: Xaa-Pro aminopeptidase
1: Xaa-Pro aminopeptidase
e: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,15715
Polymers165,3494
Non-polymers80811
Water3,243180
1
A: Xaa-Pro aminopeptidase
N: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9366
Polymers82,6752
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-160 kcal/mol
Surface area31400 Å2
MethodPISA
2
1: Xaa-Pro aminopeptidase
e: Xaa-Pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2219
Polymers82,6752
Non-polymers5477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-194 kcal/mol
Surface area29120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.600, 123.720, 136.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Xaa-Pro aminopeptidase


Mass: 41337.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sibiricus MM 739 (archaea)
Strain: MM 739 / DSM 12597 / Gene: TSIB_0821 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami(DE3) / References: UniProt: C6A2N7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growMethod: counter-diffusion / Details: Counter diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2013
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 51545 / Num. obs: 51209 / Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.48 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.881 / SU B: 31.993 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 1.928 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29593 2598 5.1 %RANDOM
Rwork0.22057 ---
obs0.22438 48609 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.763 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0 Å2
2---0.2 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11676 0 23 180 11879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911948
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.97816110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.81951464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74924540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.77152164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3491568
X-RAY DIFFRACTIONr_chiral_restr0.1270.21740
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218992
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 190 -
Rwork0.361 3301 -
obs--99.83 %
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)
13.14451.0967-0.68852.79550.34466.87450.359-0.06670.38440.1390.0884-0.2973-1.05540.9944-0.44740.1914-0.13310.07860.2003-0.07010.134731.20362.79617.353
23.2439-0.17740.35362.53742.17617.58340.17030.5847-0.0127-0.8835-0.290.1864-1.4535-0.74850.11970.41730.2092-0.03130.20680.00920.064222.79276.89437.137
33.7131-0.29161.76272.4279-1.23852.49890.15680.0276-0.3660.4649-0.1267-0.547-0.39970.4502-0.03010.2372-0.0988-0.06030.1323-0.00750.209517.001121.96622.775
42.09180.97580.56242.24061.78382.1291-0.14080.1062-0.2228-0.05550.248-0.2280.11760.4264-0.10720.12970.03680.0070.2049-0.00160.154730.122140.313.969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 370
2X-RAY DIFFRACTION2N4 - 370
3X-RAY DIFFRACTION314 - 370
4X-RAY DIFFRACTION4e4 - 370

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