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- PDB-1m5y: Crystallographic Structure of SurA, a Molecular Chaperone that Fa... -

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Basic information

Entry
Database: PDB / ID: 1m5y
TitleCrystallographic Structure of SurA, a Molecular Chaperone that Facilitates Outer Membrane Porin Folding
ComponentsSurvival protein surA
KeywordsISOMERASE / CELL CYCLE / Survival protein A / periplasmic molecular chaperone / membrane protein folding / gram negative bacteria
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
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 ...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 / Resolution: 3 Å
AuthorsBitto, E. / McKay, D.B.
CitationJournal: 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
DepositionJul 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 22, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Survival protein surA
B: Survival protein surA
C: Survival protein surA
D: Survival protein surA


Theoretical massNumber of molelcules
Total (without water)180,5284
Polymers180,5284
Non-polymers00
Water0
1
A: Survival protein surA

D: Survival protein surA

C: Survival protein surA

B: Survival protein surA


Theoretical massNumber of molelcules
Total (without water)180,5284
Polymers180,5284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation9_554x+1/2,y,z-1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
Buried area8000 Å2
ΔGint-40 kcal/mol
Surface area81860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.817, 223.406, 279.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Cell settingorthorhombic
Space group name H-MF222

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Components

#1: Protein
Survival protein surA / / E.C.5.2.1.8 / survival protein / Peptidyl-prolyl cis-trans isomerase surA / PPIase / Rotamase C


Mass: 45131.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sura / Plasmid: pTYB2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ABZ6, peptidylprolyl isomerase

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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: 3.43 Å3/Da / Density % sol: 64.19 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.75M ammonium sulphate, 100mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 303K, VAPOR DIFFUSION, HANGING DROP, temperature 303.0K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.75 Mammonium sulfate1reservoir
2100 mMsodium citrate1reservoirpH5.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.965
SYNCHROTRONSSRL BL11-120.965
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJan 1, 2002flat mirror (vertical focusing)
ADSC QUANTUM 42CCDMar 11, 2001flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(III) bent monochromator (horizontal focusing)SINGLE WAVELENGTHMx-ray1
2single crystal Si(III) bent monochromator (horizontal focusing)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 49633 / Num. obs: 45004 / % possible obs: 93.2 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 59 Å2 / Rsym value: 0.077 / Net I/σ(I): 1.62
Reflection shellResolution: 3→3.05 Å / Mean I/σ(I) obs: 3.9 / Num. unique all: 2114 / Rsym value: 0.348 / % possible all: 85.2
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 46785 / % possible obs: 92.9 % / Num. measured all: 217260 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 85.2 % / Rmerge(I) obs: 0.348

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 3→29.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1008569.15 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3753 9 %RANDOM
Rwork0.228 ---
obs0.228 41869 84.4 %-
all-49633 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.4224 Å2 / ksol: 0.311691 e/Å3
Displacement parametersBiso mean: 67.5 Å2
Baniso -1Baniso -2Baniso -3
1--17.08 Å20 Å20 Å2
2--1 Å20 Å2
3---16.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11914 0 0 0 11914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 511 10.1 %
Rwork0.331 4571 -
obs--62 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Lowest resolution: 3.11 Å / Rfactor Rfree: 0.417 / Rfactor Rwork: 0.347

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