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- PDB-6b8w: 1.9 Angstrom Resolution Crystal Structure of Cupin_2 Domain (pfam... -

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Basic information

Entry
Database: PDB / ID: 6b8w
Title1.9 Angstrom Resolution Crystal Structure of Cupin_2 Domain (pfam 07883) of XRE Family Transcriptional Regulator from Enterobacter cloacae.
ComponentsXRE family transcriptional regulator
KeywordsTRANSCRIPTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / XRE Family Transcriptional Regulator.
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding / cytosol
Similarity search - Function
: / Cupin 2, conserved barrel / Cupin domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / THIOCYANATE ION / XRE family transcriptional regulator
Similarity search - Component
Biological speciesEnterobacter cloacae subsp. cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / McChesney, C. / Grimshaw, S. / Sandoval, J. / Satchell, K.J.F. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.9 Angstrom Resolution Crystal Structure of Cupin_2 Domain (pfam 07883) of XRE Family Transcriptional Regulator from Enterobacter cloacae.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / McChesney, C. / Grimshaw, S. / Sandoval, J. / Satchell, K.J.F. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: XRE family transcriptional regulator
B: XRE family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7284
Polymers21,6152
Non-polymers1132
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 1Y9Q
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-21 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.269, 66.269, 116.319
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein XRE family transcriptional regulator


Mass: 10807.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_02024 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A0H3CJW2
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that the full length protein used in study was hydrolyzed during crystallization ...Authors state that the full length protein used in study was hydrolyzed during crystallization experiments, the model starts at 81th residue GLN of UniProt reference, but it is not known exactly where the protein was hydrolyzed.

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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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 12.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5; Screen: 0.2M Sodium thiocyan, 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 21115 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Rsym value: 0.074 / Χ2: 1.028 / Net I/σ(I): 22.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1019 / CC1/2: 0.678 / Rpim(I) all: 0.381 / Rrim(I) all: 0.87 / Rsym value: 0.779 / Χ2: 1.029 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y9Q

1y9q


Resolution: 1.9→29.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.538 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.131 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22046 1056 5 %RANDOM
Rwork0.18284 ---
obs0.18483 20005 99.66 %-
Solvent computationIon probe radii: 0.6 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.197 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.13 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1530 0 4 285 1819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191632
X-RAY DIFFRACTIONr_bond_other_d0.0020.021478
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9432228
X-RAY DIFFRACTIONr_angle_other_deg0.80233433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2855198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.57522.63276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.26515257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2891511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211832
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02351
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_it1.4562.358784
X-RAY DIFFRACTIONr_mcbond_other1.4542.353782
X-RAY DIFFRACTIONr_mcangle_it2.3943.514984
X-RAY DIFFRACTIONr_mcangle_other2.3953.518985
X-RAY DIFFRACTIONr_scbond_it1.4552.606848
X-RAY DIFFRACTIONr_scbond_other1.4542.606847
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4253.831243
X-RAY DIFFRACTIONr_long_range_B_refined7.50631.1311897
X-RAY DIFFRACTIONr_long_range_B_other7.18329.1071799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 77 -
Rwork0.253 1446 -
obs--100 %
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)
15.6716-0.24394.95711.6184-0.71136.842-0.0649-0.3601-0.09040.10330.15830.2730.0619-0.0439-0.09340.02740.03170.03220.08230.02540.08977.263627.300845.5602
21.6026-0.27490.21211.06980.61951.8260.15630.0497-0.0508-0.079-0.1242-0.0003-0.2079-0.0324-0.03210.07130.0340.00570.0498-0.01130.1073.141638.143635.7013
32.02130.99712.71582.34143.1586.42160.0983-0.041-0.14050.1654-0.04890.15220.1327-0.0618-0.04930.03630.00910.00390.0235-0.02020.0766.575332.333138.9752
41.0177-1.6687-1.1566.40843.41172.88280.1752-0.1150.1946-0.25990.0854-0.5695-0.0940.2937-0.26060.04610.0180.02440.1108-0.03990.101721.984828.379832.0755
52.4632-2.2348-0.45024.34772.24241.6297-0.1837-0.17870.06010.65610.2684-0.04210.48950.2168-0.08470.21750.1596-0.00390.197-0.00780.1120.624417.561637.9833
61.2671-1.8245-1.093.07751.43451.0007-0.208-0.30740.14530.33670.3799-0.20170.19170.3186-0.1720.14060.1439-0.03790.2029-0.05780.126720.364320.947537.1883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A81 - 99
2X-RAY DIFFRACTION2A100 - 161
3X-RAY DIFFRACTION3A162 - 175
4X-RAY DIFFRACTION4B81 - 111
5X-RAY DIFFRACTION5B112 - 143
6X-RAY DIFFRACTION6B144 - 175

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