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- PDB-2pv2: Crystallographic Structure of SurA first peptidyl-prolyl isomeras... -

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Basic information

Entry
Database: PDB / ID: 2pv2
TitleCrystallographic Structure of SurA first peptidyl-prolyl isomerase domain complexed with peptide NFTLKFWDIFRK
Components
  • C-peptide
  • Chaperone surA
KeywordsISOMERASE / Survival protein A / Peptidyl-prolyl cis-trans isomerase domain
Function / homology
Function and homology information


maintenance of stationary phase / maintenance of unfolded protein / Gram-negative-bacterium-type cell outer membrane assembly / chaperone-mediated protein folding / 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 / PPIC-type PPIASE 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 ...Peptidyl-prolyl isomerase SurA / SurA N-terminal / SurA N-terminal domain / PPIC-type PPIASE 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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsXu, X. / McKay, D.B.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The Periplasmic Bacterial Molecular Chaperone SurA Adapts its Structure to Bind Peptides in Different Conformations to Assert a Sequence Preference for Aromatic Residues.
Authors: Xu, X. / Wang, S. / Hu, Y.X. / McKay, D.B.
#1: Journal: Structure / Year: 2002
Title: Crystallographic structure of SurA, a molecular chaperone that facilitates folding of outer membrane porins
Authors: Bitto, E. / McKay, D.B.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone surA
B: Chaperone surA
C: Chaperone surA
D: Chaperone surA
E: C-peptide
F: C-peptide


Theoretical massNumber of molelcules
Total (without water)47,1456
Polymers47,1456
Non-polymers00
Water7,170398
1
A: Chaperone surA
B: Chaperone surA
E: C-peptide


Theoretical massNumber of molelcules
Total (without water)23,5733
Polymers23,5733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chaperone surA
D: Chaperone surA
F: C-peptide


Theoretical massNumber of molelcules
Total (without water)23,5733
Polymers23,5733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.46, 50.63, 74.06
Angle α, β, γ (deg.)90.000, 111.54, 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 / PPIase surA / Rotamase surA / Survival protein A


Mass: 10977.320 Da / Num. of mol.: 4 / Fragment: PPIC 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 EMG2 / Gene: surA / Plasmid: pTYB1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0ABZ6, peptidylprolyl isomerase
#2: Protein/peptide C-peptide


Mass: 1617.910 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% ployethylene glycol 8000, 0.1 M imdidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 93257 / % possible obs: 96.2 % / Redundancy: 2.5 % / Rsym value: 0.045 / Χ2: 3.377 / Net I/σ(I): 26.5
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.2 % / Num. unique all: 8714 / Rsym value: 0.25 / Χ2: 2.093 / % possible all: 90.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M5Y

1m5y


Resolution: 1.3→28.2 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 9046 9.5 %Random
Rwork0.208 ---
obs-90278 94.4 %-
Solvent computationBsol: 48.339 Å2
Displacement parametersBiso mean: 17.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.966 Å20 Å22.723 Å2
2---5.335 Å20 Å2
3---3.369 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 0 398 3722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.48
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 1.3→1.38 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.281 1357 -
Rwork0.256 --
obs-12776 89.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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