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- PDB-2w48: Crystal structure of the Full-length Sorbitol Operon Regulator So... -

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Basic information

Entry
Database: PDB / ID: 2w48
TitleCrystal structure of the Full-length Sorbitol Operon Regulator SorC from Klebsiella pneumoniae
ComponentsSORBITOL OPERON REGULATOR
KeywordsTRANSCRIPTION / SORC / ACTIVATOR / REPRESSOR / DNA-BINDING / KLEBSIELLA PNEUMONIAE / TRANSCRIPTION REGULATOR / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


DNA-templated transcription initiation / carbohydrate binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Helix-turn-helix domain / Sugar-binding domain, putative / : / Putative sugar-binding domain / Rossmann fold - #1360 / ArsR-like helix-turn-helix domain / NagB/RpiA transferase-like / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / Homeodomain-like ...Helix-turn-helix domain / Sugar-binding domain, putative / : / Putative sugar-binding domain / Rossmann fold - #1360 / ArsR-like helix-turn-helix domain / NagB/RpiA transferase-like / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Sorbitol operon regulator
Similarity search - Component
Biological speciesKLEBSIELLA PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
Authorsde Sanctis, D. / McVey, C.E. / Enguita, F.J. / Carrondo, M.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of the Full-Length Sorbitol Operon Regulator Sorc from Klebsiella Pneumoniae: Structural Evidence for a Novel Transcriptional Regulation Mechanism.
Authors: De Sanctis, D. / Mcvey, C.E. / Enguita, F.J. / Carrondo, M.A.
History
DepositionNov 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: SORBITOL OPERON REGULATOR
B: SORBITOL OPERON REGULATOR
C: SORBITOL OPERON REGULATOR
D: SORBITOL OPERON REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0319
Polymers140,5754
Non-polymers4565
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-32.5 kcal/mol
Surface area66110 Å2
MethodPQS
Unit cell
Length a, b, c (Å)91.670, 113.330, 184.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 51:55 OR RESSEQ 57:81 OR RESSEQ 91:232 OR RESSEQ 234:252 OR RESSEQ 258:312 )
211CHAIN C AND (RESSEQ 51:55 OR RESSEQ 57:81 OR RESSEQ...
112CHAIN B AND (RESSEQ 35:55 OR RESSEQ 57:82 OR RESSEQ...
212CHAIN D AND (RESSEQ 35:55 OR RESSEQ 57:82 OR RESSEQ...

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.844, 0.171, -0.508), (0.147, -0.838, -0.526), (-0.515, -0.519, 0.682)-125.136, -21.417, -45.599
2given(-0.831, 0.166, -0.53), (0.159, -0.843, -0.514), (-0.532, -0.512, 0.674)-126.46, -19.65, -46.12

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
SORBITOL OPERON REGULATOR / SORC TRANSCRIPTION REGULATOR / SOR OPERON ACTIVATOR


Mass: 35143.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) KLEBSIELLA PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37078

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Non-polymers , 5 types, 6 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.44 Å3/Da / Density % sol: 64 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 32577 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 67.68 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.6
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GNP

2gnp


Resolution: 3.2→38.672 Å / SU ML: 0.36 / σ(F): 17.58 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 1644 5.09 %
Rwork0.218 --
obs0.2194 32320 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.638 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 75.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.2→38.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9596 0 29 1 9626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149788
X-RAY DIFFRACTIONf_angle_d1.47713213
X-RAY DIFFRACTIONf_dihedral_angle_d22.7186027
X-RAY DIFFRACTIONf_chiral_restr0.0881472
X-RAY DIFFRACTIONf_plane_restr0.0071710
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1895X-RAY DIFFRACTIONPOSITIONAL
12C1895X-RAY DIFFRACTIONPOSITIONAL0.439
21B1950X-RAY DIFFRACTIONPOSITIONAL
22D1950X-RAY DIFFRACTIONPOSITIONAL0.55
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.29410.35521230.29652545X-RAY DIFFRACTION100
3.2941-3.40040.32831290.28182542X-RAY DIFFRACTION100
3.4004-3.52180.28811460.2632491X-RAY DIFFRACTION100
3.5218-3.66270.24461190.22912553X-RAY DIFFRACTION100
3.6627-3.82930.24151690.21322497X-RAY DIFFRACTION100
3.8293-4.0310.22331520.20462500X-RAY DIFFRACTION100
4.031-4.28320.22881280.19712549X-RAY DIFFRACTION100
4.2832-4.61350.19921290.18012562X-RAY DIFFRACTION100
4.6135-5.07680.20311440.17972553X-RAY DIFFRACTION100
5.0768-5.80930.24661240.2152590X-RAY DIFFRACTION100
5.8093-7.3110.26271360.21222607X-RAY DIFFRACTION100
7.311-38.67430.21531450.19712687X-RAY DIFFRACTION98
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)
10.91550.58120.22750.0540.05720.4688-0.01270.17470.16990.1228-0.02790.1826-0.3068-0.16680.05020.43860.0021-0.10570.288-0.02150.4779-62.5483-8.2184-61.8252
21.50050.38950.25380.99070.87712.087-0.0920.0198-0.0027-0.03630.00980.14860.0496-0.05650.07090.10470.0118-0.03830.1737-0.00130.2487-33.802514.7421-24.8684
30.94740.2549-0.23570.18280.67370.7862-0.0958-0.65650.09390.2728-0.12160.08250.0612-0.2220.02990.5750.1439-0.09231.0391-0.03480.819611.726217.9793-51.2868
43.63921.11960.87071.09950.37761.6883-0.17090.19380.0507-0.02240.1697-0.149-0.11880.3534-0.00270.12730.0383-0.0250.3119-0.03690.2329-3.060127.7951-12.9297
50.55420.8866-0.70950.7590.66020.3613-0.22390.909-0.6174-0.26150.5116-0.2725-0.27960.9403-0.15851.1099-0.01950.15582.0333-0.20661.13423.125624.5324-39.9006
62.1426-0.59860.79442.2995-0.09061.2790.0160.38590.2656-0.2322-0.0463-0.3698-0.04250.46480.030.5029-0.034-0.01260.69770.04980.51-22.8536.7124-63.6021
71.08760.8707-0.86290.28080.02341.2545-0.1797-0.1915-0.27640.23730.08340.20260.2752-0.15290.09190.6693-0.0323-0.14160.5328-0.15340.6783-49.3621-9.8782-53.58
83.35421.52390.61932.6346-0.37851.4921-0.06210.32960.2457-0.1468-0.01330.2456-0.15640.0050.06910.59960.1395-0.12590.5842-0.04320.4516-54.891127.3682-73.9315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 4:58
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 59:315
3X-RAY DIFFRACTION3CHAIN B AND RESSEQ 4:58
4X-RAY DIFFRACTION4CHAIN B AND RESSEQ 59:315
5X-RAY DIFFRACTION5CHAIN C AND RESSEQ 4:58
6X-RAY DIFFRACTION6CHAIN C AND RESSEQ 59:315
7X-RAY DIFFRACTION7CHAIN D AND RESSEQ 4:58
8X-RAY DIFFRACTION8CHAIN D AND RESSEQ 59:315

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