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- PDB-4pf1: Crystal structure of aminopeptidase from marine sediment archaeon... -

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Basic information

Entry
Database: PDB / ID: 4pf1
TitleCrystal structure of aminopeptidase from marine sediment archaeon Thaumarchaeota archaeon
ComponentsPeptidase S15/CocE/NonD
KeywordsHYDROLASE / serine peptidase / single cell genomics / alpha/beta hydrolase fold / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


dipeptidyl-peptidase activity
Similarity search - Function
alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / : / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like ...alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / : / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Jelly Rolls / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Peptidase S15/CocE/NonD
Similarity search - Component
Biological speciesThaumarchaeota archaeon SCGC AB-539-E09 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMichalska, K. / Chhor, G. / Fayman, K. / Endres, M. / Jedrzejczak, R. / Babnigg, G. / Steen, A. / Lloyd, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: FASEB J. / Year: 2015
Title: New aminopeptidase from "microbial dark matter" archaeon.
Authors: Michalska, K. / Steen, A.D. / Chhor, G. / Endres, M. / Webber, A.T. / Bird, J. / Lloyd, K.G. / Joachimiak, A.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.2Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase S15/CocE/NonD
B: Peptidase S15/CocE/NonD
C: Peptidase S15/CocE/NonD
D: Peptidase S15/CocE/NonD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,08723
Polymers285,1054
Non-polymers1,98219
Water20,2491124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21500 Å2
ΔGint-29 kcal/mol
Surface area81070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.434, 108.144, 120.384
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptidase S15/CocE/NonD / AP TA1 peptidase


Mass: 71276.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thaumarchaeota archaeon SCGC AB-539-E09 (archaea)
Gene: MCGE09_00221 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: M7TVE7
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1124 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Na citrate, 20% PEG3350, 2.8 mM DL-Phe

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979268 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979268 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 176913 / Num. obs: 176530 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 24.97 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3 % / Rmerge(I) obs: 0.57 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
SBC-Collectdata collection
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MPX

1mpx


Resolution: 2.1→29.69 Å / Cor.coef. Fo:Fc: 0.9089 / Cor.coef. Fo:Fc free: 0.878 / SU R Cruickshank DPI: 0.205 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.203 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.166
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 2166 1.23 %RANDOM
Rwork0.2051 ---
obs0.2054 175745 99.77 %-
Displacement parametersBiso mean: 24.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.3675 Å20 Å2-2.0413 Å2
2--2.7541 Å20 Å2
3----2.3865 Å2
Refine analyzeLuzzati coordinate error obs: 0.281 Å
Refinement stepCycle: 1 / Resolution: 2.1→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19666 0 1254 1124 22044
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00820394HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.7327758HARMONIC3
X-RAY DIFFRACTIONt_dihedral_angle_d9100SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes481HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2939HARMONIC5
X-RAY DIFFRACTIONt_it20394HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion2.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2539SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23884SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2324 148 1.14 %
Rwork0.2088 12841 -
all0.209 12989 -
obs--99.77 %
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)
10.37-0.040.15810.4182-0.18110.50390.062-0.05070.04490.0428-0.04930.0379-0.0509-0.1004-0.0127-0.02760.0006-0.0428-0.049-0.0272-0.040758.552554.3616109.0028
20.3527-0.0557-0.03830.28670.08570.4290.085-0.0217-0.06810.0354-0.0396-0.08460.04320.1085-0.0454-0.0482-0.0079-0.1303-0.05290.0350.006197.847123.3892108.7928
30.44350.05190.18310.38340.10690.57260.00910.16720.078-0.0568-0.0194-0.0763-0.11440.17050.0102-0.0616-0.0177-0.0552-0.02810.0593-0.047493.303159.493176.1488
40.34640.03910.01230.3289-0.03950.3860.06230.0861-0.1028-0.0464-0.04430.04130.0458-0.0533-0.018-0.03110.0207-0.1177-0.0435-0.0563-0.023163.018919.386275.6849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|8 - A|623}
2X-RAY DIFFRACTION2{B|7 - B|623}
3X-RAY DIFFRACTION3{C|7 - C|623}
4X-RAY DIFFRACTION4{D|8 - D|623}

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