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- PDB-1xfo: Crystal Structure of an archaeal aminopeptidase -

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Basic information

Entry
Database: PDB / ID: 1xfo
TitleCrystal Structure of an archaeal aminopeptidase
ComponentsFrv operon protein FrvX
KeywordsHYDROLASE / aminopeptidase / self-compartmentalizing / metalloprotease / dinuclear
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / Peptidase M42, domain 2 / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tetrahedral aminopeptidase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsRusso, S. / Baumann, U.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of a dodecameric tetrahedral shaped aminopeptidase
Authors: Russo, S. / Baumann, U.
History
DepositionSep 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 25, 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_ncs_dom_lim / 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_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Frv operon protein FrvX
B: Frv operon protein FrvX
C: Frv operon protein FrvX
D: Frv operon protein FrvX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,56512
Polymers158,0424
Non-polymers5238
Water11,620645
1
A: Frv operon protein FrvX
B: Frv operon protein FrvX
C: Frv operon protein FrvX
D: Frv operon protein FrvX
hetero molecules

A: Frv operon protein FrvX
B: Frv operon protein FrvX
C: Frv operon protein FrvX
D: Frv operon protein FrvX
hetero molecules

A: Frv operon protein FrvX
B: Frv operon protein FrvX
C: Frv operon protein FrvX
D: Frv operon protein FrvX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,69636
Polymers474,12612
Non-polymers1,57024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area55030 Å2
ΔGint-1197 kcal/mol
Surface area129960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.340, 158.340, 114.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11D-412-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 6 - 353 / Label seq-ID: 10 - 357

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe physiological dodecamer is generated by the three fold axis at: 1/3, 2/3, z

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Components

#1: Protein
Frv operon protein FrvX / Frvx aminopeptidase


Mass: 39510.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O59196
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.6 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 400, sodium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 11, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 110425 / Num. obs: 110425 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 24.3
Reflection shellResolution: 1.95→2.07 Å / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.2 / % possible all: 63.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHE

1vhe


Resolution: 1.96→29.92 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.51 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 2427 2.2 %RANDOM
Rwork0.18282 ---
all0.18341 110402 --
obs0.18341 107975 100 %-
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: 37.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10514 0 8 645 11167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210711
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.96514499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3651349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09324.494445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.228151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2981554
X-RAY DIFFRACTIONr_chiral_restr0.0840.21673
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027904
X-RAY DIFFRACTIONr_nbd_refined0.1950.24889
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2721
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.230
X-RAY DIFFRACTIONr_mcbond_it0.3673.56965
X-RAY DIFFRACTIONr_mcangle_it0.552310850
X-RAY DIFFRACTIONr_scbond_it0.56844287
X-RAY DIFFRACTIONr_scangle_it0.9665.53649
Refine LS restraints NCS

Ens-ID: 1 / Number: 2610 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.250.5
2Bmedium positional0.140.5
3Cmedium positional0.180.5
4Dmedium positional0.170.5
1Amedium thermal0.262
2Bmedium thermal0.282
3Cmedium thermal0.262
4Dmedium thermal0.312
LS refinement shellResolution: 1.958→1.998 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.28 100 -
Rwork0.223 3752 -
obs--100 %
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)
10.7604-0.4817-0.65491.97930.51721.4388-0.0418-0.01430.0272-0.01320.0095-0.2520.01430.21430.0323-0.25210.01620.0199-0.10020.0257-0.109543.03197.58524.833
20.964-0.20070.54780.61620.21921.4961-0.03740.10350.2223-0.1176-0.0049-0.1356-0.1620.12160.0423-0.0913-0.04650.0592-0.13430.1179-0.055227.264120.8490.673
30.84560.05490.40641.5845-0.41530.7677-0.030.2766-0.0362-0.20260.0362-0.14270.00250.1609-0.0062-0.10030.00480.13740.0024-0.0232-0.145133.8786.004-8.923
41.4993-0.6273-0.58261.32060.15130.88120.0051-0.13460.10270.1122-0.0093-0.1125-0.07790.10190.0042-0.1953-0.025-0.0408-0.1786-0.0263-0.207617.817102.83456.413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3535 - 357
2X-RAY DIFFRACTION2BB6 - 35310 - 357
3X-RAY DIFFRACTION3CC6 - 35310 - 357
4X-RAY DIFFRACTION4DD6 - 35310 - 357

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