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- PDB-6xd8: Crystal Structure of Peptidylprolyl Isomerase (PrsA) Fragment fro... -

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Basic information

Entry
Database: PDB / ID: 6xd8
TitleCrystal Structure of Peptidylprolyl Isomerase (PrsA) Fragment from Bacillus anthracis
ComponentsFoldase protein PrsA 1
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Peptidylprolyl Isomerase
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 peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Foldase protein PrsA 1
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of Peptidylprolyl Isomerase (PrsA) Fragment from Bacillus anthracis
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Foldase protein PrsA 1
B: Foldase protein PrsA 1


Theoretical massNumber of molelcules
Total (without water)22,4972
Polymers22,4972
Non-polymers00
Water2,846158
1
A: Foldase protein PrsA 1


Theoretical massNumber of molelcules
Total (without water)11,2481
Polymers11,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Foldase protein PrsA 1


Theoretical massNumber of molelcules
Total (without water)11,2481
Polymers11,2481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.889, 107.344, 31.698
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

21A-378-

HOH

31B-373-

HOH

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Components

#1: Protein Foldase protein PrsA 1 / / Peptidylprolyl Isomerase


Mass: 11248.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: prsA1, prsA-1, BA_1041, GBAA_1041, BAS0974 / Plasmid: pMCSG92 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): (DE3) magic / References: UniProt: Q81U45, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.87 Å3/Da / Density % sol: 34.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 7.8 mg/ml, 0.01M Tris pH 8.3; Screen: Classics II (H11), 0.1M Potassium thiocyanate, 30% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2020 / Details: Be
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 26434 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.025 / Rrim(I) all: 0.066 / Rsym value: 0.061 / Χ2: 1.133 / Net I/σ(I): 28.5
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1272 / CC1/2: 0.817 / CC star: 0.948 / Rpim(I) all: 0.289 / Rrim(I) all: 0.78 / Rsym value: 0.723 / Χ2: 1.006 / % 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: 1.52→27.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.513 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 1301 4.9 %RANDOM
Rwork0.1697 ---
obs0.1722 25087 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.87 Å2 / Biso mean: 23.476 Å2 / Biso min: 11.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å20 Å2
2--0.31 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 1.52→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 0 0 162 1634
Biso mean---35.63 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0131525
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181485
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.6562027
X-RAY DIFFRACTIONr_angle_other_deg0.3321.6063500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1445192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.09526.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.88415308
X-RAY DIFFRACTIONr_chiral_restr0.0560.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.021660
X-RAY DIFFRACTIONr_gen_planes_other0.0530.02268
X-RAY DIFFRACTIONr_rigid_bond_restr0.7833010
LS refinement shellResolution: 1.522→1.561 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 89 -
Rwork0.202 1791 -
all-1880 -
obs--99.47 %
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)
13.3187-1.15061.55993.3768-3.04423.7391-0.0444-0.02830.17140.1983-0.0041-0.1231-0.25950.00950.04850.041-0.00510.00050.0013-0.00240.01911.440521.271626.5388
26.06444.51883.59355.12733.08083.41860.07010.0673-0.48940.20160.0516-0.55890.30890.1611-0.12170.09680.0179-0.01950.01410.02260.138418.1873.437231.1721
32.04540.23610.07934.9357-1.20443.00760.0606-0.2405-0.13710.30090.01250.18160.0492-0.134-0.07310.0283-0.01240.00640.03680.01750.0198.570211.727234.9154
43.5063-0.28331.8372.8741-0.38572.72180.05780.1284-0.0460.014-0.0277-0.2652-0.1220.2405-0.03010.0151-0.0160.00190.032-0.00930.030518.008718.314827.2325
55.1112-2.34841.0598.7968-2.98665.85090.13620.4955-0.0987-0.1851-0.09040.23370.03290.007-0.04580.00730.0112-0.00710.051-0.00650.00788.209917.58221.1583
61.91610.60890.49943.75631.55231.34410.01330.0481-0.1288-0.17-0.01540.1941-0.1067-0.05710.00220.0158-0.0005-0.01590.01420.00880.0398-12.551510.543616.5647
72.78063.2898-0.80029.0403-3.76851.8524-0.0835-0.0635-0.0726-0.050.06030.00790.02820.00020.02320.01940.02830.0190.04580.03710.0498-8.3452-1.349318.314
82.27330.51160.62735.85762.80013.3393-0.06070.1481-0.1337-0.43430.1787-0.2114-0.12960.1564-0.1180.0364-0.01540.01430.02920.00070.0268-4.67929.665411.9968
93.79340.31121.74694.6719-0.55413.03250.0804-0.14450.13830.2664-0.15870.3098-0.0111-0.18290.07820.0182-0.0070.02210.0263-0.01320.0299-13.787616.007521.6754
105.1951.00793.36472.55321.17614.510.0590.01760.01310.0502-0.05420.052-0.0195-0.0248-0.00480.009-0.0067-0.00210.01380.01030.0142-11.266413.521418.5473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A129 - 139
2X-RAY DIFFRACTION2A140 - 158
3X-RAY DIFFRACTION3A159 - 182
4X-RAY DIFFRACTION4A183 - 216
5X-RAY DIFFRACTION5A217 - 222
6X-RAY DIFFRACTION6B129 - 150
7X-RAY DIFFRACTION7B151 - 160
8X-RAY DIFFRACTION8B161 - 183
9X-RAY DIFFRACTION9B184 - 208
10X-RAY DIFFRACTION10B209 - 222

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