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- PDB-4rpu: Crystal Structure of Human Presequence Protease in Complex with I... -

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Basic information

Entry
Database: PDB / ID: 4rpu
TitleCrystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60
Components(Presequence protease, ...) x 2
Keywordshydrolase/hydrolase inhibitor / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Mitochondrial protein import / protein targeting to mitochondrion / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / enzyme activator activity / protein processing / metalloendopeptidase activity / metallopeptidase activity / mitochondrial matrix / mitochondrion / proteolysis / zinc ion binding
Similarity search - Function
Peptidase M16C associated / Peptidase M16C associated / PreP C-terminal domain / Peptidase M16C associated / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) ...Peptidase M16C associated / Peptidase M16C associated / PreP C-terminal domain / Peptidase M16C associated / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3UE / ACETATE ION / Presequence protease, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.265 Å
AuthorsMo, S.M. / Liang, W.G. / King, J.V. / Wijaya, J. / Koehler, C.M. / Tang, W.J.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60
Authors: Mo, S.M. / Liang, W.G. / King, J.V. / Wijaya, J. / Koehler, C.M. / Tang, W.J.
History
DepositionOct 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Presequence protease, mitochondrial
B: Presequence protease, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,62036
Polymers231,6172
Non-polymers4,00334
Water14,610811
1
A: Presequence protease, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,91018
Polymers115,8241
Non-polymers2,08717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Presequence protease, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,71018
Polymers115,7941
Non-polymers1,91617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)245.624, 85.490, 158.214
Angle α, β, γ (deg.)90.00, 127.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Presequence protease, ... , 2 types, 2 molecules AB

#1: Protein Presequence protease, mitochondrial / hPreP / Pitrilysin metalloproteinase 1 / Metalloprotease 1 / hMP1


Mass: 115823.789 Da / Num. of mol.: 1 / Fragment: UNP residues 33-1037 / Mutation: E107Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PITRM1, KIAA1104, MP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5JRX3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein Presequence protease, mitochondrial / hPreP / Pitrilysin metalloproteinase 1 / Metalloprotease 1 / hMP1


Mass: 115793.695 Da / Num. of mol.: 1 / Fragment: UNP residues 33-1037 / Mutation: E107Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PITRM1, KIAA1104, MP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5JRX3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 6 types, 845 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-3UE / [4-(diphenylmethyl)piperazin-1-yl](3-methyl-4-nitrophenyl)methanone


Mass: 415.484 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H25N3O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 811 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONFLICTS ARE DUE TO GENETIC VARIATION

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 15.0% PEG 8000, 15 mM TCEP, 80 mM sodium cacodylate pH 6.7, 160 mM calcium acetate, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. all: 120522 / Num. obs: 119317 / % possible obs: 99 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.675 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.265→44.853 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 1992 1.67 %
Rwork0.1755 --
obs0.176 119303 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.265→44.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15815 0 268 811 16894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616506
X-RAY DIFFRACTIONf_angle_d0.97222350
X-RAY DIFFRACTIONf_dihedral_angle_d13.7446173
X-RAY DIFFRACTIONf_chiral_restr0.0432401
X-RAY DIFFRACTIONf_plane_restr0.0052882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2648-2.32140.3371320.25977705X-RAY DIFFRACTION91
2.3214-2.38420.27851450.2538226X-RAY DIFFRACTION98
2.3842-2.45440.27891330.23858328X-RAY DIFFRACTION98
2.4544-2.53360.29641480.22928298X-RAY DIFFRACTION98
2.5336-2.62410.27941340.22378270X-RAY DIFFRACTION98
2.6241-2.72920.29211410.21448387X-RAY DIFFRACTION99
2.7292-2.85340.23821420.20088403X-RAY DIFFRACTION99
2.8534-3.00380.2231440.18788389X-RAY DIFFRACTION99
3.0038-3.19190.20041410.18288465X-RAY DIFFRACTION100
3.1919-3.43830.19251490.16718501X-RAY DIFFRACTION100
3.4383-3.78410.2051410.1518501X-RAY DIFFRACTION100
3.7841-4.33130.15251470.14358552X-RAY DIFFRACTION100
4.3313-5.45550.17561450.14618566X-RAY DIFFRACTION100
5.4555-44.86180.18191500.16458720X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 36.4444 Å / Origin y: 53.5367 Å / Origin z: 24.4747 Å
111213212223313233
T0.3257 Å2-0.0023 Å20.0027 Å2-0.3471 Å2-0.0013 Å2--0.3565 Å2
L0.0722 °2-0.0236 °2-0.0302 °2-0.2357 °20.2967 °2--0.4924 °2
S0.0081 Å °0.0082 Å °-0.0056 Å °-0.0101 Å °-0.0285 Å °0.0271 Å °0.0084 Å °-0.0618 Å °0.0282 Å °
Refinement TLS groupSelection details: all

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