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- PDB-7l6z: Crystal Structure of Peptidyl-Prolyl Cis-Trans Isomerasefrom (Ppi... -

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Basic information

Entry
Database: PDB / ID: 7l6z
TitleCrystal Structure of Peptidyl-Prolyl Cis-Trans Isomerasefrom (PpiB) Streptococcus pneumoniae R6
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Peptidyl-prolyl Isomerase
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / Cyclophilin-like / Cyclophilin / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of Peptidyl-Prolyl Cis-Trans Isomerasefrom (PpiB) Streptococcus pneumoniae R6
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / 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
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
C: Peptidyl-prolyl cis-trans isomerase
D: Peptidyl-prolyl cis-trans isomerase
E: Peptidyl-prolyl cis-trans isomerase
F: Peptidyl-prolyl cis-trans isomerase
G: Peptidyl-prolyl cis-trans isomerase
H: Peptidyl-prolyl cis-trans isomerase
I: Peptidyl-prolyl cis-trans isomerase
J: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,01426
Polymers239,14110
Non-polymers1,87216
Water27,5271528
1
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0474
Polymers23,9141
Non-polymers1333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9853
Polymers23,9141
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3053
Polymers23,9141
Non-polymers3902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1453
Polymers23,9141
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1453
Polymers23,9141
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3053
Polymers23,9141
Non-polymers3902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9502
Polymers23,9141
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1092
Polymers23,9141
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)23,9141
Polymers23,9141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1092
Polymers23,9141
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.432, 156.529, 90.535
Angle α, β, γ (deg.)90.000, 117.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23914.137 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: ppiA, spr0679 / Plasmid: pMCSG92 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q8DQG5, peptidylprolyl isomerase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1528 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein: 5.0 mg/ml, 0.01M Tris pH 8.3;Screen: PACT (B8), 0.2M Ammonium chloride, 0.1M MES pH 6.0, 20% (w/v) PEG6000.
PH range: 6

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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: Jul 24, 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: 1.88→30 Å / Num. obs: 175455 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.045 / Rrim(I) all: 0.098 / Rsym value: 0.087 / Χ2: 1.181 / Net I/σ(I): 16.6
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8741 / CC1/2: 0.725 / CC star: 0.917 / Rpim(I) all: 0.393 / Rrim(I) all: 0.857 / Rsym value: 0.758 / Χ2: 1.001 / % possible all: 99.1

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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: 1.88→29.97 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.63 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 9021 5.1 %RANDOM
Rwork0.1728 ---
obs0.1748 166357 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.82 Å2 / Biso mean: 34.069 Å2 / Biso min: 16.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0 Å20.9 Å2
2---1.06 Å20 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 1.88→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16640 0 108 1551 18299
Biso mean--71.73 38 -
Num. residues----2132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01317211
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715702
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.65523252
X-RAY DIFFRACTIONr_angle_other_deg0.3561.58736865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.24252144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44825.446830
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.785152904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8111532
X-RAY DIFFRACTIONr_chiral_restr0.0640.22264
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.0219200
X-RAY DIFFRACTIONr_gen_planes_other0.0520.023224
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 635 -
Rwork0.273 12125 -
all-12760 -
obs--97.73 %
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)
10.809-0.035-0.18571.28030.03811.2574-0.01130.00530.0283-0.06090.03150.0341-0.0243-0.1327-0.02020.03280.0105-0.01620.06930.02480.0233-6.202338.593721.793
21.7147-4.53822.856412.0137-7.63967.6280.1371-0.0179-0.0112-0.36060.04030.02530.00830.097-0.17750.0325-0.015400.04930.02290.1112.946751.62817.498
31.18290.01-0.26281.7384-0.25781.0849-0.0411-0.0528-0.02920.00950.0202-0.18760.04120.08740.02090.0250.0136-0.01120.05870.01030.03225.373237.242823.2279
42.9124-4.29330.21916.4744-0.2360.0691-0.123-0.09510.06020.25470.0636-0.01350.0306-0.04980.05930.09850.01720.00250.15740.00470.1424-15.682945.875332.3496
54.45453.07713.71163.67290.36716.2460.2449-0.2288-0.27080.0033-0.0423-0.16250.4539-0.2993-0.20260.1210.02770.00060.10750.06460.137337.406224.26730.3554
61.33070.00350.00940.7252-0.2881.38770.00520.0067-0.0711-0.06080.0296-0.01570.03490.116-0.03480.02280.0153-0.0060.0485-0.0180.011239.652938.364919.7242
71.5416-0.42550.15691.41680.32611.50930.0326-0.0774-0.25060.01-0.00660.23570.1962-0.1937-0.0260.0366-0.0198-0.01410.04590.01620.06727.457631.215821.8666
81.4983-0.94690.55881.4378-0.1780.7459-0.01-0.05250.2032-0.03110.0304-0.1975-0.0806-0.0049-0.02040.0290.00720.01760.0947-0.00250.04841.48540.307526.5986
93.75821.35531.05225.49811.97020.80050.0133-0.2983-0.19360.3907-0.07180.27870.1263-0.08120.05850.0713-0.00850.04680.11820.01720.044521.517637.2428-6.6853
101.51080.0795-0.57920.7193-0.21161.50140.01520.0255-0.0209-0.04260.0337-0.0181-0.03540.0302-0.0490.0732-0.00780.0060.0698-0.00810.004237.418942.0016-14.4611
116.9421-1.59851.72643.8454-2.82548.6106-0.00070.1243-0.2979-0.3089-0.04750.07720.7167-0.31680.04820.1164-0.07680.03280.0771-0.0450.046322.698224.2766-17.9043
120.78970.004-0.31740.3785-0.08331.8410.05630.11450.0259-0.08230.0450.0245-0.1376-0.1245-0.10130.0514-0.00430.00010.04790.00830.007831.893644.4269-16.8641
131.68290.1344-0.38841.8160.07291.61770.14050.01230.0817-0.0635-0.134-0.0772-0.0754-0.1041-0.00650.05580.01720.00980.03390.00940.008923.262656.245846.993
149.0807-3.43913.97648.729-3.29627.75960.0871-0.2672-0.26840.6673-0.17570.4435-0.0276-0.0750.08860.1364-0.07940.04120.0715-0.00390.042216.409751.366464.5438
150.9980.27610.00511.6346-0.13531.19920.1304-0.04520.12670.0202-0.1121-0.1019-0.30030.0108-0.01830.10830.00980.02860.02520.00740.040926.811465.929148.0661
163.9082-2.76542.62081.9725-1.88613.54240.11810.12540.1885-0.0586-0.1253-0.12810.29360.1460.00720.1395-0.0273-0.01470.1220.02150.06729.914144.245550.0402
171.60450.3363-0.10051.6949-0.66951.6198-0.0313-0.1238-0.0652-0.0559-0.1181-0.2223-0.09680.10950.14940.0573-0.0078-0.00490.0230.03350.073816.342322.539745.9242
189.325-1.0366-5.39835.579-1.587112.5338-0.0655-0.62150.3370.5181-0.3124-0.318-0.74440.38670.37780.1897-0.0683-0.12210.09010.0180.089421.616426.751264.2951
191.45280.36260.20681.9368-0.35191.6137-0.045-0.1774-0.17320.0221-0.0957-0.14730.0941-0.00360.14080.04720.00110.01540.02480.02980.06211.893912.97250.9542
200.89490.3903-0.17011.7083-0.06011.10120.0109-0.0286-0.1692-0.172-0.0991-0.2880.084-0.01110.08820.050.00790.02460.02180.02760.072813.661217.910243.9532
211.5046-0.03410.36211.4772-0.35141.46370.0115-0.047-0.048-0.2133-0.0511-0.0270.0695-0.01110.03960.10470.0235-0.00220.10320.01760.0072-3.213835.0611-13.0898
224.6845-3.7239-5.02829.98457.12437.87140.09040.51970.1689-0.267-0.30850.2075-0.4419-0.29520.21810.1057-0.012-0.04550.13070.09040.08977.779855.0922-20.2162
231.21350.96510.86711.6586-0.45832.2597-0.11030.2013-0.0147-0.3039-0.0614-0.24470.13480.39580.17170.24260.0340.05780.25750.05480.16555.954640.2634-20.0797
240.38950.09860.55960.67360.06894.00240.08-0.0444-0.0438-0.1632-0.0639-0.13260.1756-0.0719-0.01610.0960.02920.02760.02980.01630.0282-1.880228.3507-11.5691
251.3922-0.4385-0.47072.45960.56391.2108-0.0417-0.08940.1425-0.02480.0895-0.1316-0.06070.0728-0.04780.04230.0220.01810.0281-0.02610.186360.202964.355927.1216
262.7422-1.5465-2.3938.1595-0.677410.5538-0.29650.0805-0.2729-0.1482-0.096-0.5779-0.37330.73970.39250.111-0.07780.05150.1112-0.00910.373579.013375.625424.9892
272.753-0.1986-0.49773.2105-0.06981.9331-0.0634-0.46390.13410.38470.1952-0.3764-0.02060.2652-0.13180.07310.0421-0.04110.1157-0.07190.212666.627865.850336.5391
280.62030.2339-0.03680.978-1.44775.7390.01580.0306-0.0537-0.0054-0.01840.1145-0.03970.09780.00270.07430.04230.00030.0481-0.04720.147351.723269.625226.2752
296.035-2.4217-4.4550.99191.79443.9206-0.2504-0.49090.2120.0960.1241-0.09550.22330.55150.12630.28350.0265-0.04470.29020.02130.310726.607469.216916.8683
301.6892-0.0402-0.37841.9114-0.02311.50040.0083-0.01940.3442-0.07390.0561-0.20220.0357-0.1295-0.06440.1009-0.02210.02130.0219-0.03630.210515.881177.62584.8792
3118.10614.046711.037821.19410.15319.49320.0878-0.09040.1078-0.4957-0.07240.08630.1678-0.1011-0.01530.1074-0.02090.03450.00970.00340.084834.618565.8683-3.2435
320.91070.475-0.3721.33030.05910.9546-0.06620.02580.1066-0.02720.0058-0.09980.2722-0.10630.06030.0986-0.03020.00190.0131-0.01980.14916.975770.46366.9289
333.2281.13420.5322.3612-0.38472.5280.08940.0391-0.4265-0.1589-0.2854-0.42150.42550.18040.1960.11570.02950.02710.05580.05510.139166.854211.534825.9055
342.97530.9789-0.55481.7948-1.56042.9469-0.0031-0.0488-0.4424-0.3532-0.0624-0.08340.6828-0.42170.06550.2741-0.1247-0.02070.15440.00440.170753.4647.078227.7725
353.33830.6754-0.12053.5041-1.2643.77130.2722-0.6895-0.28730.3256-0.4105-0.25870.0884-0.04050.13830.0867-0.1065-0.03460.18470.07670.0662.596113.826738.7659
360.56080.5195-0.18762.10693.20857.1022-0.1287-0.1022-0.2922-0.0716-0.0328-0.24420.12160.17230.16140.11530.07910.01750.08740.06310.227174.24154.013919.6429
375.6266-4.393.50783.8473-1.59725.5414-0.2144-0.4570.09460.04780.10510.0207-0.6251-0.69370.10930.4593-0.07850.00960.3672-0.10980.410128.31448.338714.8839
381.1262-0.3586-1.29091.73960.85324.1524-0.0487-0.08610.0170.1234-0.0326-0.0654-0.14620.44720.08130.0547-0.0437-0.04060.06530.02840.03437.0221-0.06952.1979
3911.06060.92630.74526.59222.561112.4647-0.2820.21420.18080.10170.12930.6548-0.0748-0.58050.15270.04550.04690.02030.0980.03470.083316.21049.98540.5917
401.140.2944-1.20581.729-0.48863.55210.1094-0.01740.07840.0178-0.0939-0.1237-0.60510.3887-0.01550.1402-0.0923-0.01040.079-0.00270.073737.44776.57833.8338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A60 - 188
2X-RAY DIFFRACTION2A189 - 200
3X-RAY DIFFRACTION3A201 - 255
4X-RAY DIFFRACTION4A256 - 273
5X-RAY DIFFRACTION5B60 - 74
6X-RAY DIFFRACTION6B75 - 194
7X-RAY DIFFRACTION7B195 - 241
8X-RAY DIFFRACTION8B242 - 272
9X-RAY DIFFRACTION9C60 - 72
10X-RAY DIFFRACTION10C73 - 191
11X-RAY DIFFRACTION11C192 - 210
12X-RAY DIFFRACTION12C211 - 272
13X-RAY DIFFRACTION13D60 - 136
14X-RAY DIFFRACTION14D137 - 149
15X-RAY DIFFRACTION15D150 - 254
16X-RAY DIFFRACTION16D255 - 273
17X-RAY DIFFRACTION17E60 - 136
18X-RAY DIFFRACTION18E137 - 149
19X-RAY DIFFRACTION19E150 - 199
20X-RAY DIFFRACTION20E200 - 272
21X-RAY DIFFRACTION21F60 - 190
22X-RAY DIFFRACTION22F191 - 200
23X-RAY DIFFRACTION23F201 - 242
24X-RAY DIFFRACTION24F243 - 272
25X-RAY DIFFRACTION25G60 - 194
26X-RAY DIFFRACTION26G195 - 207
27X-RAY DIFFRACTION27G208 - 247
28X-RAY DIFFRACTION28G248 - 272
29X-RAY DIFFRACTION29H60 - 72
30X-RAY DIFFRACTION30H73 - 194
31X-RAY DIFFRACTION31H195 - 200
32X-RAY DIFFRACTION32H201 - 272
33X-RAY DIFFRACTION33I60 - 150
34X-RAY DIFFRACTION34I151 - 219
35X-RAY DIFFRACTION35I220 - 252
36X-RAY DIFFRACTION36I253 - 272
37X-RAY DIFFRACTION37J60 - 75
38X-RAY DIFFRACTION38J76 - 194
39X-RAY DIFFRACTION39J195 - 207
40X-RAY DIFFRACTION40J208 - 272

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