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- PDB-4g2p: Crystal structure of peptidyl-prolyl cis-trans isomerase domain I... -

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Basic information

Entry
Database: PDB / ID: 4g2p
TitleCrystal structure of peptidyl-prolyl cis-trans isomerase domain II of molecular chaperone SurA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
ComponentsChaperone SurA
KeywordsISOMERASE / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / PCSEP / Program for the Characterization of Secreted Effector Proteins
Function / homology
Function and homology information


maintenance of stationary phase / Gram-negative-bacterium-type cell outer membrane assembly / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / peptide binding / unfolded protein binding / protein folding / outer membrane-bounded periplasmic space / protein stabilization
Similarity search - Function
Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / 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 / Chitinase A; domain 3 - #40 ...Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / 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 / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Roll / Alpha Beta
Similarity search - Domain/homology
Chaperone SurA / Chaperone SurA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsChang, C. / Wu, R. / Adkins, J.N. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of peptidyl-prolyl cis-trans isomerase domain II of molecular chaperone SurA from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Authors: Chang, C. / Wu, R. / Adkins, J.N. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionJul 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone SurA
B: Chaperone SurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4236
Polymers24,0472
Non-polymers3764
Water3,351186
1
A: Chaperone SurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3044
Polymers12,0231
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chaperone SurA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1192
Polymers12,0231
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.499, 39.611, 68.581
Angle α, β, γ (deg.)90.000, 101.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chaperone SurA / Peptidyl-prolyl cis-trans isomerase SurA / Rotamase SurA


Mass: 12023.388 Da / Num. of mol.: 2 / Fragment: UNP residues 280-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S (bacteria)
Strain: 14028s / SGSC 2262 / Gene: surA, STM14_0111 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D0ZJR9, UniProt: A0A0F6AWM7*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Lithium sulfate, 0.1M Bis-Tris, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 20735 / Num. obs: 20486 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 34.3
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.7 / Num. unique all: 930 / % possible all: 90.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M5Y

1m5y


Resolution: 1.82→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 8.575 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 1052 5.1 %RANDOM
Rwork0.1612 ---
all0.1652 20476 --
obs0.1652 20476 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.32 Å2 / Biso mean: 39.0817 Å2 / Biso min: 19.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å2-5.04 Å2
2---3.99 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1660 0 22 186 1868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021751
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9582377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56124.52173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03915294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.435158
X-RAY DIFFRACTIONr_chiral_restr0.090.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211312
X-RAY DIFFRACTIONr_rigid_bond_restr3.57231751
X-RAY DIFFRACTIONr_sphericity_free36.799572
X-RAY DIFFRACTIONr_sphericity_bonded23.61751827
LS refinement shellResolution: 1.821→1.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 84 -
Rwork0.197 1239 -
all-1323 -
obs-1323 88.49 %
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)
10.16320.0599-0.05630.0245-0.02190.02010.00540.01640.0048-0.0071-0.00230.00560.0046-0.0031-0.00310.0757-0.0001-0.00830.0620.00480.073514.47234.777210.5513
21.1072-0.3833-0.65861.4169-1.0291.62240.01670.08130.0038-0.1061-0.01180.0040.0948-0.0613-0.00490.0859-0.0083-0.01510.0846-0.00810.07462.5767-0.8899-9.475
30.6054-0.13230.06880.0626-0.22131.27480.02560.0017-0.0157-0.0038-0.00310.0050.0080.0214-0.02250.07460.0032-0.00850.0776-0.01070.09764.3208-11.53752.3914
40.28830.2504-0.15461.59290.04240.10560.0064-0.0052-0.00250.0006-0.0025-0.0302-0.00670.0029-0.00390.0809-0.0025-0.01120.0871-0.00060.080715.0064-6.0591-0.5132
51.0720.3105-0.50894.9574.44454.6401-0.03640.01220.0462-0.09150.1434-0.0295-0.03920.1712-0.10690.07610.0156-0.01010.0875-0.01960.061519.7129-2.57954.7245
62.9861-2.04961.21551.4165-0.82310.66480.05820.04350.0217-0.011-0.0333-0.02130.0235-0.0112-0.02490.0839-0.012-0.01070.07330.00250.051914.45939.659610.0018
73.2621-1.88711.60391.0966-0.92760.7891-0.1124-0.10950.15220.04380.0419-0.0874-0.0494-0.05930.07050.07280.02040.01620.0909-0.03280.07947.28767.881710.4043
80.4151-0.21740.44230.1172-0.23720.48160.0096-0.0042-0.02130.00670.01040.0144-0.0107-0.0203-0.020.063-0.0024-0.00140.0788-0.00980.07558.50172.02099.5274
94.8691-1.3756.24230.3888-1.76298.0027-0.10980.87090.40670.0042-0.3318-0.1171-0.03571.11740.44160.06080.03610.03340.20610.09030.138830.552-3.9915-17.8193
100.04890.0141-0.05540.00940.04680.8357-0.0597-0.0178-0.0125-0.0276-0.0188-0.0028-0.0736-0.13430.07860.11140.0216-0.01430.08930.0050.09327.10128.3586-22.2993
111.58671.39590.47581.6553-0.06840.6983-0.0114-0.02940.02070.02650.03270.043-0.0494-0.0716-0.02130.05640.0031-0.00240.06580.00650.07062.613113.4463-31.2774
120.8091-0.19510.56210.1834-0.5331.5626-0.02580.00770.0190.0333-0.0039-0.0198-0.06570.00360.02970.1150.0025-0.03750.0356-0.00180.068111.978821.7211-24.8289
130.12050.03820.46830.01290.1531.8482-0.0203-0.03810.0006-0.00470.0036-0.0003-0.0821-0.12890.01670.07280.0105-0.01270.07680.00890.08926.050912.9044-16.7631
140.1789-0.13180.34110.0978-0.25280.6537-0.09170.03840.05580.0659-0.0243-0.0457-0.170.06130.1160.0662-0.0078-0.01010.0725-0.00280.071418.48126.5326-15.7784
150.28690.3913-0.39310.6931-0.28520.9989-0.0115-0.0158-0.01290.011-0.0368-0.04010.02970.01860.04830.06580.0003-0.01440.0740.00550.083416.8656-0.3759-25.0629
160.533-0.02020.22020.00240.01070.33330.00220.0111-0.0101-0.0028-0.00290.0014-0.03460.00910.00080.07550.0028-0.01180.07350.00260.073217.13567.1853-25.9383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 293
2X-RAY DIFFRACTION2A294 - 306
3X-RAY DIFFRACTION3A307 - 319
4X-RAY DIFFRACTION4A320 - 334
5X-RAY DIFFRACTION5A335 - 342
6X-RAY DIFFRACTION6A343 - 352
7X-RAY DIFFRACTION7A353 - 358
8X-RAY DIFFRACTION8A359 - 386
9X-RAY DIFFRACTION9B279 - 284
10X-RAY DIFFRACTION10B285 - 297
11X-RAY DIFFRACTION11B298 - 313
12X-RAY DIFFRACTION12B314 - 324
13X-RAY DIFFRACTION13B325 - 336
14X-RAY DIFFRACTION14B337 - 346
15X-RAY DIFFRACTION15B347 - 358
16X-RAY DIFFRACTION16B359 - 386

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