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- PDB-1nrz: Crystal structure of the IIBSor domain of the sorbose permease fr... -

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Basic information

Entry
Database: PDB / ID: 1nrz
TitleCrystal structure of the IIBSor domain of the sorbose permease from Klebsiella pneumoniae solved to 1.75A resolution
ComponentsPTS system, sorbose-specific IIB component
KeywordsTRANSFERASE / BETA SHEET CORE / FLANKING HELICES / RIGHT HANDED BETA-ALPHA-BETA CROSSOVER
Function / homology
Function and homology information


protein-Npi-phosphohistidine-L-sorbose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm
Similarity search - Function
Phosphotransferase system, sorbose subfamily IIB component, subgroup / Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system sorbose-specific EIIB component
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOrriss, G.L. / Erni, B. / Schirmer, T.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of the IIBSor domain of the sorbose permease from Klebsiella pneumoniae solved to 1.75A resolution
Authors: Orriss, G.L. / Erni, B. / Schirmer, T.
History
DepositionJan 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTS system, sorbose-specific IIB component
B: PTS system, sorbose-specific IIB component
C: PTS system, sorbose-specific IIB component
D: PTS system, sorbose-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2978
Polymers73,9134
Non-polymers3844
Water8,431468
1
A: PTS system, sorbose-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6703
Polymers18,4781
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PTS system, sorbose-specific IIB component


Theoretical massNumber of molelcules
Total (without water)18,4781
Polymers18,4781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PTS system, sorbose-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5742
Polymers18,4781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PTS system, sorbose-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5742
Polymers18,4781
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
A: PTS system, sorbose-specific IIB component
B: PTS system, sorbose-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1494
Polymers36,9572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-43 kcal/mol
Surface area16080 Å2
MethodPISA
6
C: PTS system, sorbose-specific IIB component
D: PTS system, sorbose-specific IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1494
Polymers36,9572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-40 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.848, 85.311, 67.815
Angle α, β, γ (deg.)90.00, 103.02, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological monomer, but there are four copies in the asymmetric unit

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Components

#1: Protein
PTS system, sorbose-specific IIB component / EIIB-SOR / Sorbose-permease IIB component / Phosphotransferase enzyme II / B component / EIII-B-SOR


Mass: 18478.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: SORB / Plasmid: pMSFBAM470 / Production host: Escherichia coli (E. coli) / Strain (production host): WA2127deltaG
References: UniProt: P37081, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.32 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 19-25% PEG 8000, 0.2M ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114-19 mg/mlprotein1drop
20.2 Mammonium sulfate1reservoir
321 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 8, 2001 / Details: MIRRORS
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→21.38 Å / Num. all: 72155 / Num. obs: 72155 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 20.16 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 9.5
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.1 / Num. unique all: 15789 / Rsym value: 0.235 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 68518

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BLE cut down to common atoms

1ble


Resolution: 1.75→21.37 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.105 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24268 3637 5 %RANDOM
Rwork0.21593 ---
obs0.21731 68518 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.907 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å20.83 Å2
2---0.95 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.75→21.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 20 468 5636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225168
X-RAY DIFFRACTIONr_bond_other_d0.0010.024840
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9517032
X-RAY DIFFRACTIONr_angle_other_deg0.722311204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9963648
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6415943
X-RAY DIFFRACTIONr_chiral_restr0.0820.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025684
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02976
X-RAY DIFFRACTIONr_nbd_refined0.2380.31104
X-RAY DIFFRACTIONr_nbd_other0.2020.34599
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5365
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0870.55
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3620.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3640.524
X-RAY DIFFRACTIONr_mcbond_it0.4861.53254
X-RAY DIFFRACTIONr_mcangle_it0.92825292
X-RAY DIFFRACTIONr_scbond_it1.64831914
X-RAY DIFFRACTIONr_scangle_it2.7694.51740
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 269
Rwork0.266 5022
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)
10.707-0.42410.12361.6493-0.22760.7765-0.0374-0.010.0556-0.0103-0.0144-0.003-0.0841-0.06120.05180.0232-0.0026-0.03240.0762-0.01340.0499-5.2950.5227.472
20.65-0.1686-0.05811.69580.38070.86580.00240.01180.0084-0.03480.0226-0.1517-0.02290.0966-0.0250.01050.0057-0.02860.07850.01250.08822.648-6.37927.555
31.72220.5465-0.86692.26630.23052.1182-0.02180.10740.02950.02880.0540.054-0.004-0.0211-0.03220.1790.0397-0.00160.11580.01090.0597-12.8139.11460.358
42.025-0.6621-1.70141.50880.78934.3810.0465-0.3768-0.09330.03-0.0806-0.09620.03290.31570.03410.1326-0.0604-0.03830.21880.03980.08515.2740.40960.399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1641 - 163
2X-RAY DIFFRACTION2BB2 - 1641 - 163
3X-RAY DIFFRACTION3CC2 - 1641 - 163
4X-RAY DIFFRACTION4DD2 - 1641 - 163
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.34

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