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- PDB-5tpi: 1.47 Angstrom Crystal Structure of the C-terminal Substrate Bindi... -

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Basic information

Entry
Database: PDB / ID: 5tpi
Title1.47 Angstrom Crystal Structure of the C-terminal Substrate Binding Domain of LysR Family Transcriptional Regulator from Klebsiella pneumoniae.
ComponentsPutative transcriptional regulator (LysR family)
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyLysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / Putative transcriptional regulator (LysR family)
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsMinasov, G. / Wawrzak, Z. / Sandoval, J. / Evdokimova, E. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.47 Angstrom Crystal Structure of the C-terminal Substrate Binding Domain of LysR Family Transcriptional Regulator from Klebsiella pneumoniae.
Authors: Minasov, G. / Wawrzak, Z. / Sandoval, J. / Evdokimova, E. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator (LysR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3295
Polymers23,2121
Non-polymers1174
Water3,747208
1
A: Putative transcriptional regulator (LysR family)
hetero molecules

A: Putative transcriptional regulator (LysR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,65910
Polymers46,4252
Non-polymers2348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3750 Å2
ΔGint-116 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.756, 40.228, 68.211
Angle α, β, γ (deg.)90.00, 129.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-303-

NA

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Components

#1: Protein Putative transcriptional regulator (LysR family)


Mass: 23212.410 Da / Num. of mol.: 1 / Fragment: UNP residues 85-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: yneJ, KPN_01634 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A6T8Z4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 18.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5, Screen: 3.2M NaCl, 0.1M Bis-Tris-propane (pH=7.0); Cryo: Paratone.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2016 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.47→30 Å / Num. obs: 33672 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 35.8
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.837 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→26.35 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.234 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 1662 5 %RANDOM
Rwork0.13674 ---
obs0.13886 31890 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.584 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-0.65 Å2
2--4.16 Å20 Å2
3----1.53 Å2
Refinement stepCycle: 1 / Resolution: 1.47→26.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 4 208 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191778
X-RAY DIFFRACTIONr_bond_other_d0.0020.021674
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9472444
X-RAY DIFFRACTIONr_angle_other_deg0.88633848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.155235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.1082275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40715280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6381516
X-RAY DIFFRACTIONr_chiral_restr0.0990.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0212094
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02440
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_it1.531895
X-RAY DIFFRACTIONr_mcbond_other1.527894
X-RAY DIFFRACTIONr_mcangle_it2.0621142
X-RAY DIFFRACTIONr_mcangle_other2.0621143
X-RAY DIFFRACTIONr_scbond_it2.366883
X-RAY DIFFRACTIONr_scbond_other2.366883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8451301
X-RAY DIFFRACTIONr_long_range_B_refined3.9322072
X-RAY DIFFRACTIONr_long_range_B_other3.4312023
X-RAY DIFFRACTIONr_rigid_bond_restr1.631645
X-RAY DIFFRACTIONr_sphericity_free25.4065103
X-RAY DIFFRACTIONr_sphericity_bonded11.34651659
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 119 -
Rwork0.249 2337 -
obs--99.68 %
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)
10.70410.2469-0.32860.7583-0.32110.6545-0.0235-0.0344-0.0570.0145-0.0218-0.07620.01120.06620.04540.00170.0015-0.00080.00710.00560.027635.86198.92241.0369
20.8134-0.03970.05020.437-0.19190.84830.01760.0287-0.02010.0205-0.00470.0564-0.0221-0.0961-0.0130.00180.00240.00070.0144-0.0060.033311.930213.39135.0902
31.13980.6797-0.76620.4283-0.3840.94340.1102-0.19060.04160.0767-0.11360.004-0.11380.11640.00340.0662-0.0076-0.02130.0343-0.0080.089336.62214.5548.5569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 156
2X-RAY DIFFRACTION2A157 - 262
3X-RAY DIFFRACTION3A263 - 292

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