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- PDB-1miq: Crystal structure of proplasmepsin from the human malarial pathog... -

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Basic information

Entry
Database: PDB / ID: 1miq
TitleCrystal structure of proplasmepsin from the human malarial pathogen Plasmodium vivax
Componentsplasmepsin
KeywordsHYDROLASE / aspartic proteinase zymogen / domain opening
Function / homology
Function and homology information


food vacuole / aspartic-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(malaria parasite P. vivax) hypothetical protein
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBernstein, N.K. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural insights into the activation of P. vivax plasmepsin.
Authors: Bernstein, N.K. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N.
History
DepositionAug 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 24, 2018Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: plasmepsin
B: plasmepsin


Theoretical massNumber of molelcules
Total (without water)85,5192
Polymers85,5192
Non-polymers00
Water1,13563
1
A: plasmepsin


Theoretical massNumber of molelcules
Total (without water)42,7591
Polymers42,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: plasmepsin


Theoretical massNumber of molelcules
Total (without water)42,7591
Polymers42,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.409, 92.735, 99.132
Angle α, β, γ (deg.)90.00, 130.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein plasmepsin / aspartic proteinase


Mass: 42759.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The 122-residue prosegment has been truncated to 48 residues
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O60989
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18% PEG 4000, 100 mM Tris, 200 mM ammonium acetate, 3% t-amyl alcohol, 15 % glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 394K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 117641 / Num. obs: 116818 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.27 % / Biso Wilson estimate: 62.1 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.5
Reflection shellResolution: 2.5→2.54 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1QS8 and 1PFZ

1qs8

1pfz


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.376 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.409 / ESU R Free: 0.264
RfactorNum. reflection% reflectionSelection details
Rfree0.24534 1852 5.2 %RANDOM
Rwork0.20322 ---
obs0.20535 33805 99.29 %-
all-35657 --
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: 18.297 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å2-1.23 Å2
2--3.4 Å20 Å2
3----3.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.265 Å0.412 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5969 0 0 63 6032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.521.9548294
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2393746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.684151105
X-RAY DIFFRACTIONr_chiral_restr0.0960.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024617
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2610.32941
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.5870
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.332
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6871.53719
X-RAY DIFFRACTIONr_mcangle_it1.30126040
X-RAY DIFFRACTIONr_scbond_it1.91332399
X-RAY DIFFRACTIONr_scangle_it3.0994.52254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 122
Rwork0.238 2484
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)
12.7271.2949-0.28061.38630.36382.2999-0.030.0741-0.11880.0242-0.02920.07260.29270.03780.05920.4730.0189-0.00970.3141-0.08030.510346.0272-1.37882.723
227.888924.01071.720753.886614.535830.6792-0.27351.35731.5759-0.26720.4073.01061.3144-2.2137-0.13350.1277-0.18520.12750.54870.15540.540517.8127-11.505810.198
319.97212.1066-10.34540.6085-1.38714.9631-0.6149-0.9214-1.29650.0394-0.0999-0.39330.13890.2090.71480.4813-0.01340.08430.3951-0.06440.511714.4825-19.573726.2917
45.2994-1.0581-0.57690.81570.77253.2022-0.3633-0.5960.23050.03490.2465-0.1137-0.1010.02520.11680.524-0.01420.00480.4373-0.14270.4254-10.9841-13.066135.5115
56.4446-1.172-2.61973.45151.77714.9457-0.3921-1.56490.91-0.25370.4529-0.6702-0.15391.0494-0.06080.3525-0.0293-0.10190.7851-0.31360.611615.2405-9.739237.2493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA78 - 111126 - 159
2X-RAY DIFFRACTION1AA3 - 32751 - 375
3X-RAY DIFFRACTION2AA112 - 2160 - 50
4X-RAY DIFFRACTION3BB76 - 123124 - 171
5X-RAY DIFFRACTION4BB1 - 19749 - 245
6X-RAY DIFFRACTION4BB301 - 327349 - 375
7X-RAY DIFFRACTION5BB198 - 300246 - 348

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