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- PDB-4l3t: Crystal Structure of Substrate-free Human Presequence Protease -

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Basic information

Entry
Database: PDB / ID: 4l3t
TitleCrystal Structure of Substrate-free Human Presequence Protease
Components(Presequence protease, ...) x 2
KeywordsHYDROLASE / zinc metalloendoprotease / mitochondrial matrix
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 / 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 ...Peptidase M16C associated / Peptidase M16C associated / 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
ACETATE ION / Presequence protease, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement/SAD / Resolution: 2.03 Å
AuthorsKing, J.V. / Liang, W.G. / Tang, W.J.
CitationJournal: Structure / Year: 2014
Title: Molecular basis of substrate recognition and degradation by human presequence protease.
Authors: King, J.V. / Liang, W.G. / Scherpelz, K.P. / Schilling, A.B. / Meredith, S.C. / Tang, W.J.
History
DepositionJun 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Jul 9, 2014Group: Database references
Revision 1.4Jul 23, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)234,46424
Polymers232,9212
Non-polymers1,54322
Water19,0601058
1
A: Presequence protease, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0339
Polymers116,4551
Non-polymers5788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Presequence protease, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,43115
Polymers116,4661
Non-polymers96514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)245.782, 85.093, 158.459
Angle α, β, γ (deg.)90.00, 127.54, 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: 116454.930 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: KIAA1104, MP1, PITRM1 / Plasmid: pProExH6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q5JRX3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein Presequence protease, mitochondrial / hPreP / Pitrilysin metalloproteinase 1 / Metalloprotease 1 / hMP1


Mass: 116465.914 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: KIAA1104, MP1, PITRM1 / Plasmid: pProExH6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q5JRX3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 4 types, 1080 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1058 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsI328V, A397V, AND Q1037R ARE NATURAL VARIANTS.

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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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15.2% w/v PEG8000, 15 mM TCEP, 80 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate, 20% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 113.5 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 166830 / Num. obs: 163827 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.13 % / Biso Wilson estimate: 27.23 Å2 / Rsym value: 0.086 / Net I/σ(I): 17.1
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.75 / Num. unique all: 8053 / Rsym value: 0.585 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: molecular replacement/SAD / Resolution: 2.03→42.547 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 21.36 / Stereochemistry target values: ML
Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO- ...Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO-CRYSTALLIZATION OF TWO CHEMICALLY DISTINCT PROTEINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 7469 5 %RANDOM
Rwork0.1707 ---
obs0.1726 149417 89.29 %-
all-166830 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.486 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 36.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.6303 Å20 Å23.3484 Å2
2--5.0352 Å20 Å2
3----3.4049 Å2
Refinement stepCycle: LAST / Resolution: 2.03→42.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15806 0 96 1058 16960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116370
X-RAY DIFFRACTIONf_angle_d0.98822198
X-RAY DIFFRACTIONf_dihedral_angle_d13.7946144
X-RAY DIFFRACTIONf_chiral_restr0.0742396
X-RAY DIFFRACTIONf_plane_restr0.0042866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.05330.2972750.22551495X-RAY DIFFRACTION28
2.0533-2.07750.24251090.20681985X-RAY DIFFRACTION38
2.0775-2.10280.2761400.21062404X-RAY DIFFRACTION46
2.1028-2.12950.29351540.22263062X-RAY DIFFRACTION58
2.1295-2.15750.24721900.21193819X-RAY DIFFRACTION72
2.1575-2.1870.2542440.21084436X-RAY DIFFRACTION84
2.187-2.21830.26552410.21544856X-RAY DIFFRACTION92
2.2183-2.25140.24662590.20494949X-RAY DIFFRACTION94
2.2514-2.28660.25382670.19655068X-RAY DIFFRACTION96
2.2866-2.3240.23852700.19045115X-RAY DIFFRACTION97
2.324-2.36410.25152700.19835222X-RAY DIFFRACTION98
2.3641-2.40710.23052920.18675107X-RAY DIFFRACTION98
2.4071-2.45340.24532680.18995185X-RAY DIFFRACTION98
2.4534-2.50350.24762620.18635228X-RAY DIFFRACTION98
2.5035-2.55790.22942660.18895168X-RAY DIFFRACTION98
2.5579-2.61740.22812830.18525165X-RAY DIFFRACTION99
2.6174-2.68280.25832700.18235206X-RAY DIFFRACTION98
2.6828-2.75540.23692620.17325251X-RAY DIFFRACTION99
2.7554-2.83640.20942860.17345210X-RAY DIFFRACTION98
2.8364-2.9280.22432750.17035200X-RAY DIFFRACTION99
2.928-3.03260.19272680.16435253X-RAY DIFFRACTION99
3.0326-3.1540.2182840.1655259X-RAY DIFFRACTION99
3.154-3.29750.18282790.15255211X-RAY DIFFRACTION99
3.2975-3.47120.19452780.14685257X-RAY DIFFRACTION99
3.4712-3.68860.16592700.14285293X-RAY DIFFRACTION99
3.6886-3.97320.18192710.14585239X-RAY DIFFRACTION99
3.9732-4.37270.1852850.14435305X-RAY DIFFRACTION99
4.3727-5.00460.18142830.14485324X-RAY DIFFRACTION99
5.0046-6.30190.20192750.18875337X-RAY DIFFRACTION99
6.3019-42.55580.21252930.19445339X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 84.7848 Å / Origin y: 56.4114 Å / Origin z: -38.4891 Å
111213212223313233
T0.0317 Å20.0072 Å20.0049 Å2-0.0409 Å2-0.0174 Å2--0.0395 Å2
L0.0472 °2-0.0043 °20.0013 °2-0.0771 °20.1003 °2--0.1671 °2
S0.0122 Å °0.0042 Å °-0.0002 Å °-0.0113 Å °-0.0175 Å °0.0051 Å °-0.0135 Å °-0.049 Å °0.0056 Å °
Refinement TLS groupSelection details: all

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