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- PDB-4hvt: Structure of a Post-proline cleaving enzyme from Rickettsia typhi -

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Basic information

Entry
Database: PDB / ID: 4hvt
TitleStructure of a Post-proline cleaving enzyme from Rickettsia typhi
ComponentsPost-proline cleaving enzyme
KeywordsHYDROLASE / SSGCID / Post-proline cleaving enzyme / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / post-proline cleavage protein
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol
Similarity search - Function
: / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Post-proline cleaving enzyme
Similarity search - Component
Biological speciesRickettsia typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structure of a Post-proline cleaving enzyme from Rickettsia typhi
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Fox III, D. / Edwards, T.E. / Staker, B.L.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / Item: _pdbx_diffrn_reflns_shell.percent_possible_obs
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Post-proline cleaving enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6709
Polymers82,2271
Non-polymers4438
Water13,439746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.590, 73.280, 55.460
Angle α, β, γ (deg.)90.000, 98.520, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1386-

HOH

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Components

#1: Protein Post-proline cleaving enzyme / RityA.17583.b


Mass: 82226.664 Da / Num. of mol.: 1 / Fragment: N-terminal truncation (UNP residues 19-720)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia typhi (bacteria) / Strain: ATCC VR-144 / Wilmington / Gene: ppcE, RT0165 / Plasmid: RityA.17583.b.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q68XJ3, prolyl oligopeptidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4450
22.2846
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2901vapor diffusion, sitting drop8.5Microlyic MCSG1 screen b10: 24% PEG 4000, 20% Glycerol, 160mM Magnesium Chloride, 80mM Tris:HCl pH 8.5; RityA17583bB2.PS01616 at 26.6mg/ml, cryo: EG; SG C2; for phasing crystal 2 was used SG P21, VAPOR DIFFUSION, SITTING DROP, temperature 290K
2902vapor diffusion, sitting drop7.5Microlyic MCSG1 screen c5: 20% PEG 3350, 200mM Magnesium acetate; RityA17583bB2.PS01616 at 26.6mg/ml, for phasing a crystal was soaked in reservoir + 20% EG with 2.5M sodium iodide (final 500mM NaI) for 1 minute, this sample is from a differet space group (P21) than crystal 1, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONALS 5.0.110.9774
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDOct 14, 2012
RIGAKU SATURN 944+2CCDOct 17, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal, cylindrically bent, Si(220)SINGLE WAVELENGTHMx-ray1
2RIGAKU VariMaxSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97741
21.54181
ReflectionNumber: 305759 / Rmerge(I) obs: 0.05 / D res high: 2.1 Å / Num. obs: 84077 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
9.395091095.510.03
6.649.39170298.710.033
5.426.64219798.910.037
4.75.42267499.610.033
4.24.7300599.810.032
3.834.2332899.910.037
3.553.83361999.810.039
3.323.55387799.910.042
3.133.32417210010.041
2.973.13436810010.047
2.832.97461799.910.053
2.712.83475710010.062
2.62.71508499.910.078
2.512.6515210010.072
2.422.51541410010.081
2.352.42562299.910.084
2.282.35577099.910.097
2.212.28583999.510.126
2.152.21615699.910.11
2.12.1558149310.111
ReflectionResolution: 1.7→50 Å / Num. all: 87031 / Num. obs: 86126 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 23.221 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.86
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.740.4933.423080663481,298
1.74-1.790.3994.222969561291,298.5
1.79-1.840.325.152912559851,298.6
1.84-1.90.2526.532822557921,298.6
1.9-1.960.1968.32736456391,298.7
1.96-2.030.15710.122652454581,298.6
2.03-2.110.12912.082566952861,299
2.11-2.190.10414.412468751081,299.1
2.19-2.290.08916.322370048991,298.8
2.29-2.40.07917.892256546691,299.3
2.4-2.530.07119.622148744671,299
2.53-2.690.06222.092039142361,299.7
2.69-2.870.05524.671900439781,299.4
2.87-3.10.04528.471755636941,299.6
3.1-3.40.03833.061617534241,299.5
3.4-3.80.03337.541439831031,299.5
3.8-4.390.03238.851233527371,299.3
4.39-5.380.02841.761117323351,299.7
5.38-7.60.0338.87871218181,299.5
7.6-500.02542.91475110211,298.7

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MADD res high: 2.1 Å / D res low: 46.03 Å / FOM : 0.416 / FOM acentric: 0.429 / FOM centric: 0.128 / Reflection: 43000 / Reflection acentric: 41043 / Reflection centric: 1776
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å20 Å
Translation3.5 Å20 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: An initial model was obtained from iodide SAD phasing using crystal 2 (P21). The initial model was then used as search model for C2 high resolution data set, crystal 1.

Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1996 / WRfactor Rwork: 0.1636 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8714 / SU B: 3.886 / SU ML: 0.067 / SU R Cruickshank DPI: 0.099 / SU Rfree: 0.1011 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 4322 5 %RANDOM
Rwork0.1704 ---
all0.1723 87031 --
obs0.1723 81804 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.98 Å2 / Biso mean: 19.2341 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.54 Å2
2--0.79 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 26 746 6282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.025739
X-RAY DIFFRACTIONr_bond_other_d0.0010.025324
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9517804
X-RAY DIFFRACTIONr_angle_other_deg0.85312259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67324.583264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9971519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021357
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 331 -
Rwork0.228 5994 -
all-6325 -
obs-6348 98.03 %
Refinement TLS params.Method: refined / Origin x: 23.725 Å / Origin y: 61.672 Å / Origin z: 16.053 Å
111213212223313233
T0.0536 Å20.0113 Å2-0.0666 Å2-0.0092 Å2-0.0115 Å2--0.085 Å2
L0.4637 °20.0058 °20.2563 °2-0.529 °2-0.0524 °2--0.5823 °2
S-0.0773 Å °-0.0259 Å °0.0877 Å °-0.015 Å °0.027 Å °0.0072 Å °-0.0651 Å °-0.0668 Å °0.0504 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 710
2X-RAY DIFFRACTION1A801 - 808

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