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- PDB-1n5b: Crystal Structure Of The Yersinia enterocolitica Molecular Chaper... -

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Basic information

Entry
Database: PDB / ID: 1n5b
TitleCrystal Structure Of The Yersinia enterocolitica Molecular Chaperone Syce
ComponentsYOPE regulator
KeywordsCHAPERONE / yersinia enterocolitica / molecular chaperone / type III secretion system
Function / homologyType III secretion chaperone SycE / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / protein secretion by the type III secretion system / 2-Layer Sandwich / Alpha Beta / YopE regulator
Function and homology information
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTrame, C.B. / McKay, D.B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of the Yersinia enterocolitica molecular-chaperone protein SycE.
Authors: Trame, C.B. / McKay, D.B.
#1: Journal: NAT.STRUCT.BIOL. / Year: 2001
Title: Structure of the Yersinia Type III Secretory System Chaperone Syce
Authors: Birtalan, S. / Ghosh, P.
#2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2002
Title: Three-Dimensional Structure of the Type III Secretion Chaperone SycE from Yersinia Pestis
Authors: Evdokimov, A.G. / Tropea, J.E. / Routzahn, K.M. / Waugh, D.S.
#3: Journal: MOL.CELL / Year: 2002
Title: Three-Dimensional Secretion Signals in Chaperone-Effector Complexes of Bacterial Pathogens
Authors: Birtalan, S.C. / Phillips, R.M. / Ghosh, P.
History
DepositionNov 5, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionNov 20, 2002ID: 1MD1
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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: YOPE regulator
B: YOPE regulator
C: YOPE regulator
D: YOPE regulator


Theoretical massNumber of molelcules
Total (without water)59,3594
Polymers59,3594
Non-polymers00
Water1,60389
1
A: YOPE regulator
B: YOPE regulator


Theoretical massNumber of molelcules
Total (without water)29,6802
Polymers29,6802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-21 kcal/mol
Surface area14130 Å2
MethodPISA
2
C: YOPE regulator
D: YOPE regulator


Theoretical massNumber of molelcules
Total (without water)29,6802
Polymers29,6802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-19 kcal/mol
Surface area14020 Å2
MethodPISA
3
A: YOPE regulator
B: YOPE regulator

C: YOPE regulator
D: YOPE regulator


Theoretical massNumber of molelcules
Total (without water)59,3594
Polymers59,3594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area7770 Å2
ΔGint-48 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.550, 92.670, 101.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthere are 4 molecules in AU, packed as 2 dimers with an ncs translation peak in the native patterson (0.5,~0.,0.5)

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Components

#1: Protein
YOPE regulator / secretion chaperone SycE


Mass: 14839.753 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: YERA / Plasmid: pTYB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31490
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.17 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PEG 400, ammonium sulphate, sodium chloride, hepes, TCEP, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2002
Details: vertical focusing flat mirror, single crystal Si(111) bent monochromator (horizontal focussing)
RadiationMonochromator: horizontally focusing bent Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.98→45.72 Å / Num. obs: 34752 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 30.6
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 4 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5 / Rsym value: 0.235 / % possible all: 89.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREP(CCP4)phasing
CNS1.1refinement
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K6Z

1k6z


Resolution: 2→29.54 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1519681.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3223 9.9 %RANDOM
Rwork0.248 ---
obs0.248 32538 95.4 %-
all-32546 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8009 Å2 / ksol: 0.357917 e/Å3
Displacement parametersBiso mean: 48.4 Å2
Baniso -1Baniso -2Baniso -3
1--7.28 Å20 Å20 Å2
2--8.92 Å20 Å2
3----1.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 0 89 4039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
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: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 510 10.1 %
Rwork0.3 4545 -
obs--90.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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