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- PDB-1z5h: Crystal structures of the Tricorn interacting Factor F3 from Ther... -

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Basic information

Entry
Database: PDB / ID: 1z5h
TitleCrystal structures of the Tricorn interacting Factor F3 from Thermoplasma acidophilum
ComponentsTricorn protease interacting factor F3
KeywordsHYDROLASE / Zinc aminopeptidase / Gluzicins / Tricorn protease / Superhelix
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / metalloaminopeptidase activity / peptide binding / proteolysis / extracellular space / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / 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 ...Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Tricorn protease-interacting factor F3
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKyrieleis, O.J.P. / Goettig, P. / Kiefersauer, R. / Huber, R. / Brandstetter, H.
CitationJournal: J.MOL.BIOL. / Year: 2005
Title: Crystal Structures of the Tricorn Interacting Factor F3 from Thermoplasma acidophilum, a Zinc Aminopeptidase in Three Different Conformations
Authors: Kyrieleis, O.J.P. / Goettig, P. / Kiefersauer, R. / Huber, R. / Brandstetter, H.
History
DepositionMar 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Tricorn protease interacting factor F3
B: Tricorn protease interacting factor F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,74921
Polymers178,9852
Non-polymers1,76419
Water14,034779
1
A: Tricorn protease interacting factor F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,80715
Polymers89,4931
Non-polymers1,31414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tricorn protease interacting factor F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9426
Polymers89,4931
Non-polymers4505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Tricorn protease interacting factor F3
hetero molecules

A: Tricorn protease interacting factor F3
hetero molecules

B: Tricorn protease interacting factor F3
hetero molecules

B: Tricorn protease interacting factor F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,49942
Polymers357,9714
Non-polymers3,52838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation1_645x+1,y-1,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10330 Å2
ΔGint-593 kcal/mol
Surface area123440 Å2
MethodPISA
4
A: Tricorn protease interacting factor F3
hetero molecules

B: Tricorn protease interacting factor F3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,74921
Polymers178,9852
Non-polymers1,76419
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4290 Å2
ΔGint-279 kcal/mol
Surface area62590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.200, 183.300, 105.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Tricorn protease interacting factor F3


Mass: 89492.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Plasmid: pRset6c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
References: UniProt: O93655, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 2000, lithium sulphate, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.005 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 16, 2003
RadiationMonochromator: graphit / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.3→19.5 Å / Num. all: 99537 / Num. obs: 99516 / % possible obs: 99.9 % / Biso Wilson estimate: 24.6 Å2
Reflection shellResolution: 2.3→2.44 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4087184.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 5029 5.1 %RANDOM
Rwork0.225 ---
obs0.225 -99.8 %-
all-99537 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.8232 Å2 / ksol: 0.343331 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12590 0 87 779 13456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 843 5.1 %
Rwork0.296 15570 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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