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- PDB-7l75: Crystal Structure of Peptidylprolyl Isomerase PrsA from Streptoco... -

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Basic information

Entry
Database: PDB / ID: 7l75
TitleCrystal Structure of Peptidylprolyl Isomerase PrsA from Streptococcus mutans.
ComponentsFoldase protein PrsA
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Peptidylprolyl Isomerase / PrsA
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / protein folding / plasma membrane
Similarity search - Function
PPIC-type PPIASE domain / Foldase protein PrsA / : / Trigger factor/SurA domain superfamily / 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
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Wawrzak, Z. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of Peptidylprolyl Isomerase PrsA from Streptococcus mutans.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Wawrzak, Z. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 20, 2024Group: Structure summary / Category: 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: Foldase protein PrsA
B: Foldase protein PrsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,52310
Polymers61,8332
Non-polymers6898
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-42 kcal/mol
Surface area32020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.786, 66.207, 90.247
Angle α, β, γ (deg.)90.000, 113.110, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Foldase protein PrsA


Mass: 30916.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: ATCC 700610 / UA159 / Gene: prsA / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: Q8CVC6, peptidylprolyl isomerase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein: 8.0 mg/ml, 0.01M Tris HCl (pH 8.3);Screen: PEG's II (A11), 0.2M Magnesium chloride, 0.1M HEPES (pH 7.5), 30% (w/v) PEG 4000.
PH range: 7.5

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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: Oct 18, 2018 / Details: Be
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. obs: 12763 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 126.3 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.029 / Rrim(I) all: 0.063 / Rsym value: 0.056 / Χ2: 1.064 / Net I/σ(I): 29
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 621 / CC1/2: 0.753 / CC star: 0.927 / Rpim(I) all: 0.389 / Rrim(I) all: 0.892 / Rsym value: 0.801 / Χ2: 0.993 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TVL

5tvl


Resolution: 3.15→29.46 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / SU B: 92.399 / SU ML: 0.674 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3097 611 4.8 %RANDOM
Rwork0.2657 ---
obs0.2679 12118 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 277.82 Å2 / Biso mean: 155.275 Å2 / Biso min: 104.83 Å2
Baniso -1Baniso -2Baniso -3
1--3.9 Å20 Å27.08 Å2
2---6.2 Å2-0 Å2
3---2.97 Å2
Refinement stepCycle: final / Resolution: 3.15→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 36 0 4234
Biso mean--201.18 --
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134286
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184180
X-RAY DIFFRACTIONr_angle_refined_deg1.11.6525751
X-RAY DIFFRACTIONr_angle_other_deg0.2831.6039719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.7245531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.89125.508187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg4.31515843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.242158
X-RAY DIFFRACTIONr_chiral_restr0.0450.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.024737
X-RAY DIFFRACTIONr_gen_planes_other0.0490.02871
LS refinement shellResolution: 3.15→3.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 48 -
Rwork0.376 885 -
all-933 -
obs--100 %
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)
120.47271.6255-21.22186.81546.866133.10591.2561.4764-0.1315-1.32920.0352-0.8461-3.1353-1.4787-1.29120.42650.02550.06050.5568-0.0871.197128.900555.038-5.3091
25.0082-4.80942.388811.86760.78786.524-0.3659-0.4010.32760.26660.0938-1.76160.1342-0.14250.27210.41270.0703-0.26680.96110.05530.731921.047935.267913.6141
35.33571.0886-0.93364.16280.03320.1787-0.1549-0.1482-0.44580.10910.0922-0.42670.02010.08180.06271.1790.2002-0.53091.39160.09270.38838.496632.311719.0591
411.86292.66990.56934.89070.20747.0938-0.3029-0.0903-0.427-0.0894-0.02880.16140.5761-0.14420.33180.76960.0372-0.08380.5832-0.1560.4924-18.80825.596823.381
514.08761.7999-0.46945.16650.93772.64450.1602-0.31310.3860.5368-0.74290.19620.4327-0.37820.58270.7020.0233-0.17720.5258-0.28880.4388-17.22629.76524.4569
68.34413.2494-6.46291.7101-2.84468.58640.0014-0.3492-0.23110.760.2309-0.5519-0.8514-0.3725-0.23231.46770.2761-0.79511.5327-0.14780.715813.062439.624428.1339
72.2834-0.58131.56335.5105-3.29686.1092-0.1890.23730.1362-0.65870.2358-1.4170.4931-0.0605-0.04680.2209-0.1470.03190.7997-0.1380.691424.425557.9271-5.2287
83.4871-2.1169-1.53087.4562.439410.5795-0.62530.105-0.03570.49870.459-0.61380.5541-0.60270.16630.3928-0.2131-0.13110.9977-0.04790.145912.557268.809-11.4317
914.8841-0.00951.9062.50660.08111.2744-0.03731.06790.7993-0.9244-0.38540.4107-0.5304-0.18430.42281.08330.1736-0.23550.35390.0330.5989-12.679671.9522-30.1203
107.99811.0961-5.69862.90210.42374.82070.36470.16540.8319-0.787-0.09520.267-0.95760.0581-0.26951.1154-0.1235-0.35960.5589-0.05920.8094-16.047577.3278-26.4449
1118.9571-3.6382-0.666.1773-0.90598.21750.0593-0.79340.3459-0.35010.23990.5447-0.5759-0.1219-0.29920.6022-0.1962-0.29460.5103-0.2230.4789-17.234571.3279-22.8981
123.78230.7262.00730.41380.44334.163-0.03940.590.2695-0.70630.1759-0.30430.8714-0.2079-0.13652.4905-0.21660.40421.9905-0.19360.990513.242662.0313-28.1753
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 54
2X-RAY DIFFRACTION2A55 - 85
3X-RAY DIFFRACTION3A86 - 150
4X-RAY DIFFRACTION4A151 - 208
5X-RAY DIFFRACTION5A209 - 237
6X-RAY DIFFRACTION6A238 - 294
7X-RAY DIFFRACTION7B29 - 85
8X-RAY DIFFRACTION8B86 - 131
9X-RAY DIFFRACTION9B132 - 167
10X-RAY DIFFRACTION10B168 - 211
11X-RAY DIFFRACTION11B212 - 237
12X-RAY DIFFRACTION12B238 - 294

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