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- PDB-6vj4: 1.70 Angstrom Resolution Crystal Structure of Peptidylprolyl Isom... -

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Basic information

Entry
Database: PDB / ID: 6vj4
Title1.70 Angstrom Resolution Crystal Structure of Peptidylprolyl Isomerase (PrsA) from Bacillus anthracis
ComponentsPeptidylprolyl isomerase PrsA
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / PrsA / foldase
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / plasma membrane
Similarity search - Function
Foldase protein PrsA / Trigger factor/SurA domain superfamily / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Foldase protein PrsA 2
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Wiersum, G. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.70 Angstrom Resolution Crystal Structure of Peptidylprolyl Isomerase (PrsA) from Bacillus anthracis
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Wiersum, G. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidylprolyl isomerase PrsA


Theoretical massNumber of molelcules
Total (without water)30,3171
Polymers30,3171
Non-polymers00
Water3,279182
1
A: Peptidylprolyl isomerase PrsA

A: Peptidylprolyl isomerase PrsA


Theoretical massNumber of molelcules
Total (without water)60,6352
Polymers60,6352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1270 Å2
ΔGint-13 kcal/mol
Surface area26510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.679, 39.086, 32.171
Angle α, β, γ (deg.)90.000, 94.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptidylprolyl isomerase PrsA / Foldase protein PrsA 2


Mass: 30317.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: prsA2, prsA-2, BA_1169, GBAA_1169, BAS1084 / Plasmid: pMCSG92 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3)magic / References: UniProt: Q81TU1, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density meas: 45.2 Mg/m3 / Density % sol: 43.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 11.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Reservoir (Classics II screen, D7): 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2019 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 29240 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.031 / Rrim(I) all: 0.067 / Rsym value: 0.059 / Χ2: 1.165 / Net I/σ(I): 23.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1408 / CC1/2: 0.815 / CC star: 0.948 / Rpim(I) all: 0.388 / Rrim(I) all: 0.87 / Rsym value: 0.777 / Χ2: 1.001 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→26.44 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.019 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1446 5 %RANDOM
Rwork0.1855 ---
obs0.187 27652 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 145.1 Å2 / Biso mean: 48.152 Å2 / Biso min: 18.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.4 Å2
2--0.88 Å20 Å2
3----1.4 Å2
Refinement stepCycle: final / Resolution: 1.7→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 0 193 1930
Biso mean---42.94 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171743
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.6522442
X-RAY DIFFRACTIONr_angle_other_deg0.3081.6034113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3685228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.12926.78287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.83315377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.318152
X-RAY DIFFRACTIONr_chiral_restr0.0540.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.022010
X-RAY DIFFRACTIONr_gen_planes_other0.0560.02308
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 102 -
Rwork0.278 2000 -
all-2102 -
obs--99.95 %
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)
19.9163-5.72256.94853.3231-4.349612.6392-0.2266-0.26120.3240.12950.0919-0.203-0.37470.49060.13460.0525-0.09290.03550.427-0.0070.0917100.191134.0772-0.1663
20.03250.38070.47847.12032.901810.69980.0223-0.0106-0.00680.42440.1269-0.0898-0.06850.0383-0.14910.115-0.0733-0.04310.2577-0.04450.060992.260749.38048.5633
35.37155.17136.25746.03785.87577.4062-0.07260.03390.1467-0.0006-0.15660.1243-0.0470.18250.22920.1221-0.07450.03710.357-0.00830.151588.472736.2105-4.6221
41.30350.5001-0.95750.74390.36961.90980.007-0.0081-0.10770.1134-0.0444-0.096-0.0328-0.03620.03740.1587-0.0034-0.02950.07070.02140.041263.829913.86815.4943
51.04050.3912-0.73483.4559-2.16512.8807-0.0593-0.01620.0398-0.12510.0427-0.1284-0.0029-0.00910.01660.0586-0.00920.00140.02040.00250.010466.105516.5398-3.755
610.47770.32046.56171.9043-0.29944.68850.325-0.90940.32130.0018-0.3089-0.06380.037-0.2825-0.01620.1263-0.14580.06940.2487-0.10680.152981.119129.9265-4.1805
70.4841-0.9198-2.42033.2894.378712.6778-0.0191-0.0172-0.05950.165-0.0277-0.07170.1190.21910.04670.0561-0.0337-0.05040.068-0.03860.1758100.167723.4416-2.0989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A54 - 70
2X-RAY DIFFRACTION2A71 - 107
3X-RAY DIFFRACTION3A108 - 127
4X-RAY DIFFRACTION4A128 - 186
5X-RAY DIFFRACTION5A187 - 233
6X-RAY DIFFRACTION6A234 - 259
7X-RAY DIFFRACTION7A260 - 270

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