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- PDB-2pv3: Crystallographic Structure of SurA fragment lacking the second pe... -

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Basic information

Entry
Database: PDB / ID: 2pv3
TitleCrystallographic Structure of SurA fragment lacking the second 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 unfolded protein / Gram-negative-bacterium-type cell outer membrane assembly / : / peptide binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / protein folding / outer membrane-bounded periplasmic space / protein stabilization
Similarity search - Function
Triger factor/SurA peptide-binding fold / Porin chaperone SurA, peptide-binding domain / 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. ...Triger factor/SurA peptide-binding fold / Porin chaperone SurA, peptide-binding domain / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.39 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: Derived calculations / Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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

Downloads & links

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Assembly

Deposited unit
A: Chaperone surA
B: Chaperone surA
C: C-peptide


Theoretical massNumber of molelcules
Total (without water)68,0613
Polymers68,0613
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-32 kcal/mol
Surface area31310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)148.33, 148.33, 188.68
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Chaperone surA / Peptidyl-prolyl cis-trans isomerase surA / PPIase surA / Rotamase surA / Survival protein A


Mass: 33221.621 Da / Num. of mol.: 2
Fragment: Survivial protein A fragment from which the second peptidyl-prolyl isomerase domain has been deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 EMG2 / Gene: surA / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0ABZ6, peptidylprolyl isomerase
#2: Protein/peptide C-peptide


Mass: 1617.910 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4~1.8M sodium chloride, 0.1M potassium dihydrogen phosphate, 0.1 M sodium dihydrogen phosphate, 0.1M MES buffer, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-111
SYNCHROTRONALS 4.2.220.9790, 0.9794, 0.9950
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 21, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791
30.97941
40.9951
ReflectionResolution: 3.39→50 Å / Num. obs: 33486 / % possible obs: 99.1 % / Redundancy: 4.2 % / Rsym value: 0.074 / Net I/σ(I): 17.5
Reflection shellResolution: 3.39→3.52 Å / Redundancy: 3.5 % / Num. unique all: 3326 / Rsym value: 0.422 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
d*TREKdata scaling
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1M5Y

1m5y


Resolution: 3.39→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.908 / SU B: 22.754 / SU ML: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.501 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1690 5.1 %RANDOM
Rwork0.284 ---
obs0.284 33271 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 171.417 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å2-1.1 Å20 Å2
2---2.2 Å20 Å2
3---3.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.396 Å0.501 Å
Refinement stepCycle: LAST / Resolution: 3.39→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 0 0 4529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224650
X-RAY DIFFRACTIONr_bond_other_d0.0010.024287
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9526257
X-RAY DIFFRACTIONr_angle_other_deg0.78239977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54625.417240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73515879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9011538
X-RAY DIFFRACTIONr_chiral_restr0.0660.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025196
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
X-RAY DIFFRACTIONr_nbd_refined0.250.21349
X-RAY DIFFRACTIONr_nbd_other0.1760.25048
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22252
X-RAY DIFFRACTIONr_nbtor_other0.0840.23011
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1490.235
LS refinement shellResolution: 3.39→3.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 143 -
Rwork0.48 2237 -
obs-2380 96.51 %

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