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- PDB-3c8g: Crystal structure of a possible transciptional regulator YggD fro... -

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Basic information

Entry
Database: PDB / ID: 3c8g
TitleCrystal structure of a possible transciptional regulator YggD from Shigella flexneri 2a str. 2457T
Components(Putative transcriptional regulator) x 3
KeywordsTRANSCRIPTION REGULATOR / APC27974 / YggD / Mannitol operon repressor / Shigella flexneri 2a str. 2457T / methylation / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase
Similarity search - Function
Mannitol repressor MtlR-like / MtlR-like superfamily / Mannitol repressor / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Fumarase E
Similarity search - Component
Biological speciesShigella flexneri 2a str. 2457T (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsTan, K. / Borovilos, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The mannitol operon repressor MtlR belongs to a new class of transcription regulators in bacteria.
Authors: Tan, K. / Clancy, S. / Borovilos, M. / Zhou, M. / Horer, S. / Moy, S. / Volkart, L.L. / Sassoon, J. / Baumann, U. / Joachimiak, A.
History
DepositionFeb 12, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 19, 2008ID: 2HKT
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Putative transcriptional regulator
B: Putative transcriptional regulator
C: Putative transcriptional regulator
D: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5805
Polymers79,5214
Non-polymers591
Water21612
1
A: Putative transcriptional regulator
hetero molecules

A: Putative transcriptional regulator
hetero molecules


  • defined by author&software
  • 39.9 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)39,9054
Polymers39,7872
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1770 Å2
ΔGint-19 kcal/mol
Surface area17120 Å2
MethodPISA
2
B: Putative transcriptional regulator
C: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)39,7872
Polymers39,7872
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-18 kcal/mol
Surface area17350 Å2
MethodPISA
3
D: Putative transcriptional regulator

D: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)39,6792
Polymers39,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area2080 Å2
ΔGint-20 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.365, 70.946, 159.037
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative transcriptional regulator


Mass: 19893.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 2457T (bacteria)
Species: Shigella flexneri / Strain: 2457T / Serotype 2a / Gene: yggD, S3120, SF2919 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q83Q96
#2: Protein Putative transcriptional regulator


Mass: 19893.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 2457T (bacteria)
Species: Shigella flexneri / Strain: 2457T / Serotype 2a / Gene: yggD, S3120, SF2919 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q83Q96
#3: Protein Putative transcriptional regulator


Mass: 19839.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 2457T (bacteria)
Species: Shigella flexneri / Strain: 2457T / Serotype 2a / Gene: yggD, S3120, SF2919 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q83Q96
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% (w/v) PEG MME 2000, 0.1M Sodium acetate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97883 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 29, 2006 / Details: Mirrors
RadiationMonochromator: Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2.5→32 Å / Num. all: 26162 / Num. obs: 26162 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 71.63 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 30.78
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.88 / Num. unique all: 2140 / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→31.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 27.471 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.767 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27034 2020 7.7 %RANDOM
Rwork0.20669 ---
all0.21163 24064 --
obs0.21163 24064 93.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.751 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.27 Å2
2--0.13 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5334 0 4 12 5350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225449
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9757419
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.81725.349258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.75915822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3321516
X-RAY DIFFRACTIONr_chiral_restr0.1260.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024137
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.22490
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23735
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.2100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.53358
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22325310
X-RAY DIFFRACTIONr_scbond_it1.87732376
X-RAY DIFFRACTIONr_scangle_it2.8814.52109
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 122 -
Rwork0.292 1406 -
obs-1528 74.9 %
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)
12.96290.1263-1.31260.921-0.34784.548-0.1220.15550.1568-0.1072-0.03660.10870.3742-0.26620.1586-0.0070.11530.0754-0.1563-0.0577-0.2026.257-0.27960.493
22.25280.1173-0.17591.3407-0.08343.4864-0.0565-0.03170.33740.1739-0.0030.1332-0.07470.56610.0595-0.01460.1567-0.00730.0089-0.1194-0.089312.575-3.82623.529
31.4888-0.827-0.12131.2401-0.71154.65070.0695-0.1004-0.0599-0.16560.045-0.20140.43730.7664-0.1145-0.0178-0.11470.0230.08410.00550.030720.517-2.017-16.43
41.7432-1.5695-0.53442.3067-1.03336.45920.0099-0.2475-0.16710.1120.0590.4089-0.8279-0.3097-0.06890.0477-0.1127-0.023-0.26060.04880.077830.542-1.882-60.16
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1683 - 171
2X-RAY DIFFRACTION2BB3 - 1686 - 171
3X-RAY DIFFRACTION3CC0 - 1683 - 171
4X-RAY DIFFRACTION4DD2 - 1685 - 171

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