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- PDB-6ndi: Crystal Structure of the Sugar Binding Domain of LacI Family Prot... -

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Basic information

Entry
Database: PDB / ID: 6ndi
TitleCrystal Structure of the Sugar Binding Domain of LacI Family Protein from Klebsiella pneumoniae
ComponentsTranscriptional regulator
KeywordsSUGAR BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Periplasmic Binding / Sugar Binding
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
LacI family DNA-binding transcriptional regulator
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMinasov, G. / Shuvalova, L. / Wawrzak, Z. / Kiryukhina, O. / Dubrovska, I. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.
Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / ...Authors: Inniss, N.L. / Kochan, T.J. / Minasov, G. / Wawrzak, Z. / Chang, C. / Tan, K. / Shuvalova, L. / Kiryukhina, O. / Pshenychnyi, S. / Wu, R. / Dubrovska, I. / Babnigg, G. / Endres, M. / Anderson, W.F. / Hauser, A.R. / Joachimiak, A. / Satchell, K.J.F.
History
DepositionDec 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Structure summary / Category: citation / database_2 / struct
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Jun 14, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator
B: Transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)73,8762
Polymers73,8762
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-27 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.737, 110.478, 37.777
Angle α, β, γ (deg.)90.00, 97.94, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 61 - 330 / Label seq-ID: 64 - 333

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Transcriptional regulator


Mass: 36938.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: AN676_0312450 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) magic / References: UniProt: A0A2W0LW10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 3.0 mg/ml, 0.01M Tris-HCl pH 8.3; Screen: Classics II (C1), 3.5M Sodium formate pH 7.0; Cryo: 4.0M Sodium formate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2018 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 22623 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.049 / Rrim(I) all: 0.124 / Rsym value: 0.114 / Χ2: 1.469 / Net I/σ(I): 19.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1122 / CC1/2: 0.867 / Rpim(I) all: 0.342 / Rrim(I) all: 0.875 / Rsym value: 0.804 / Χ2: 1.024 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 21.924 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.497 / ESU R Free: 0.28 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23513 1007 4.5 %RANDOM
Rwork0.18222 ---
obs0.18447 21591 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.782 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å2-0.7 Å2
2---2.25 Å20 Å2
3---1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.6→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 0 157 4373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134320
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174012
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.6475894
X-RAY DIFFRACTIONr_angle_other_deg0.3681.5679288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.8885542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.46820.783230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.98815651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8781538
X-RAY DIFFRACTIONr_chiral_restr0.0660.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.024877
X-RAY DIFFRACTIONr_gen_planes_other0.0480.02901
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7644.1562174
X-RAY DIFFRACTIONr_mcbond_other2.7644.1572173
X-RAY DIFFRACTIONr_mcangle_it4.7566.2322714
X-RAY DIFFRACTIONr_mcangle_other4.7556.2312715
X-RAY DIFFRACTIONr_scbond_it2.7064.5212145
X-RAY DIFFRACTIONr_scbond_other2.7064.5212145
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6486.6693180
X-RAY DIFFRACTIONr_long_range_B_refined8.75549.6664671
X-RAY DIFFRACTIONr_long_range_B_other8.71849.614648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8472 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 69 -
Rwork0.313 1576 -
obs--98.44 %
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)
10.4709-1.5859-0.55255.34491.86020.6706-0.09640.0504-0.17480.331-0.1570.57810.1136-0.00660.25340.15490.003-0.02550.17070.03850.217314.8361-8.67164.6591
23.1063-2.1721-0.95821.84230.86260.417-0.0199-0.1259-0.65930.2088-0.0740.30420.154-0.02620.09380.38690.0016-0.05210.15620.0870.253619.8938-21.70264.6504
30.2861-0.08310.29881.73150.53510.571-0.0487-0.0470.0610.0030.0702-0.18860.0476-0.0315-0.02150.39710.01110.00480.01220.00360.173248.1977-15.80895.1718
42.7516-0.2965-0.93870.25450.11350.33350.26730.4864-0.0549-0.2956-0.2298-0.0779-0.0965-0.173-0.03750.49110.2073-0.00440.21370.0620.157327.9745-14.2613-6.192
50.1678-0.7119-0.54483.22692.34831.78260.04070.0483-0.0938-0.2964-0.34490.3353-0.2006-0.15760.30410.2197-0.0325-0.07690.17970.06940.185315.60945.67485.2979
63.0173-0.92833.20823.6724-2.60264.1857-0.17140.41760.574-0.1636-0.17970.3792-0.06270.48240.35110.307-0.0159-0.12110.12320.07660.25717.345918.53056.0256
70.8286-0.179-0.39331.74610.70080.42590.02140.0514-0.06130.03680.0378-0.1378-0.039-0.0123-0.05930.42-0.016-0.03050.00980.01330.141146.327813.497314.4455
81.64070.10930.84220.6566-0.11560.49640.2114-0.13010.05790.3137-0.19550.06380.1107-0.0281-0.01580.5071-0.12-0.01660.06890.00360.068427.24288.916419.3554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 126
2X-RAY DIFFRACTION2A127 - 162
3X-RAY DIFFRACTION3A163 - 292
4X-RAY DIFFRACTION4A293 - 331
5X-RAY DIFFRACTION5B61 - 129
6X-RAY DIFFRACTION6B130 - 159
7X-RAY DIFFRACTION7B160 - 285
8X-RAY DIFFRACTION8B286 - 331

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