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- PDB-7l6y: Crystal Structure of the Peptidyl-Prolyl Cis-Trans Isomerase (Ppi... -

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Basic information

Entry
Database: PDB / ID: 7l6y
TitleCrystal Structure of the Peptidyl-Prolyl Cis-Trans Isomerase (PpiB) from Streptococcus pyogenes.
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Peptidylprolyl Isomerase
Function / homologyCyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Peptidyl-prolyl cis-trans isomerase
Function and homology information
Biological speciesStreptococcus pyogenes MGAS5005 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.28 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of the Peptidyl-Prolyl Cis-Trans Isomerase (PpiB) from Streptococcus pyogenes.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)46,8352
Polymers46,8352
Non-polymers00
Water9,080504
1
A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)23,4181
Polymers23,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)23,4181
Polymers23,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.251, 50.532, 106.977
Angle α, β, γ (deg.)90.000, 92.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 23417.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS5005 (bacteria)
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q1JI83, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein: 8.8 mg/ml, 0.01M Tris HCl (pH 8.3);Screen: Classics II (D10), 0.1M Bis-Tris (pH 6.5), 20% (w/v) PEG5000 MME.
PH range: 6.5

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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: Mar 22, 2019 / Details: Be
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.28→30 Å / Num. obs: 92003 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.03 / Rrim(I) all: 0.085 / Rsym value: 0.079 / Χ2: 2.027 / Net I/σ(I): 37.1
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 3 / Num. unique obs: 4451 / CC1/2: 0.91 / Rpim(I) all: 0.303 / Rrim(I) all: 0.855 / Rsym value: 0.799 / Χ2: 1.004 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.28→27.12 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.784 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 4603 5 %RANDOM
Rwork0.1584 ---
obs0.1602 87382 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.01 Å2 / Biso mean: 18.803 Å2 / Biso min: 8.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.01 Å2
2---0.49 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.28→27.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 0 543 3779
Biso mean---29.48 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133515
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173184
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.6544776
X-RAY DIFFRACTIONr_angle_other_deg0.4731.5887488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6855462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74825.233172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.17415590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.734158
X-RAY DIFFRACTIONr_chiral_restr0.0670.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.050.024084
X-RAY DIFFRACTIONr_gen_planes_other0.0480.02684
X-RAY DIFFRACTIONr_rigid_bond_restr8.83636699
LS refinement shellResolution: 1.28→1.314 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 333 -
Rwork0.231 6212 -
all-6545 -
obs--95.09 %
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)
11.9291-0.95130.7711.8355-0.59322.5868-0.01250.10990.1827-0.06390.0043-0.1908-0.23460.35540.00820.0351-0.03850.03060.0577-0.00670.084-6.64289.196910.4466
21.5061-0.3477-0.45021.29630.31370.9897-0.0323-0.1222-0.01430.00740.02230.02240.0378-0.02370.010.00370.00360.00390.0350.00610.0066-16.6601-2.057517.4418
31.3611-0.3516-0.87450.6750.581.6260.02220.09180.0165-0.0693-0.03680.0168-0.0492-0.14710.01460.01460.00930.0090.06640.00440.0182-20.50151.06059.5682
40.7727-0.30010.3270.7283-0.21751.19010.03470.0603-0.0534-0.0777-0.0042-0.06470.06890.0421-0.03050.02220.00390.02360.0622-0.00430.0428-10.0346-5.30415.2314
53.7883-1.8501-1.71792.48390.8621.39420.04610.10670.26860.1495-0.0393-0.0665-0.1964-0.0152-0.00680.1044-0.0101-0.00890.0701-0.02940.0938-13.876812.658121.802
61.42950.8720.84191.65250.46351.86120.0379-0.07620.14180.0032-0.05950.1477-0.3107-0.19690.02160.08830.02920.02460.04780.01180.099-29.490233.288942.8593
71.01750.0049-0.48471.27330.00591.1877-0.00160.0801-0.023-0.03750.0012-0.0253-0.0580.11240.00040.0064-0.00860.00560.0354-0.00260.0113-20.528121.219636.4265
81.12380.3899-0.89640.7481-0.17821.56370.0418-0.0678-0.01080.0147-0.0249-0.0504-0.11170.2112-0.0170.013-0.02030.00980.0661-0.00320.0237-15.109825.102442.6133
90.5140.16950.1470.74120.36581.15790.0367-0.0211-0.04590.0422-0.03120.06080.01990.0412-0.00550.011-0.00130.01590.03120.0010.0483-26.240418.74648.2504
103.93943.0852-1.61094.0803-0.85361.0723-0.00270.05870.1632-0.20110.03260.0815-0.10650.0296-0.030.10840.00140.00230.10520.07150.0651-22.650436.84131.3744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 81
2X-RAY DIFFRACTION2A82 - 143
3X-RAY DIFFRACTION3A144 - 193
4X-RAY DIFFRACTION4A194 - 258
5X-RAY DIFFRACTION5A259 - 268
6X-RAY DIFFRACTION6B60 - 81
7X-RAY DIFFRACTION7B82 - 139
8X-RAY DIFFRACTION8B140 - 193
9X-RAY DIFFRACTION9B194 - 258
10X-RAY DIFFRACTION10B259 - 268

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