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- PDB-2ijl: The structure of a putative ModE from Agrobacterium tumefaciens. -

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Basic information

Entry
Database: PDB / ID: 2ijl
TitleThe structure of a putative ModE from Agrobacterium tumefaciens.
ComponentsMolybdenum-binding transcriptional repressor
KeywordsTRANSCRIPTION / molybdenum-binding / transcriptional repressor / structural genomics / DNA-binding protein / Agrobacterium tumefaciens / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Molybdenum-binding transcriptional repressor / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsCuff, M.E. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a putative ModE from Agrobacterium tumefaciens.
Authors: Cuff, M.E. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 30, 2024Group: 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: Molybdenum-binding transcriptional repressor
B: Molybdenum-binding transcriptional repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,12016
Polymers30,9792
Non-polymers1,14114
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-134 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.719, 79.536, 43.994
Angle α, β, γ (deg.)90.00, 106.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Molybdenum-binding transcriptional repressor / AGR_C_4647p


Mass: 15489.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: modE / Plasmid: p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8UCD4, UniProt: A9CHN1*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M LiSO4, 0.1M Bis-Tris ph 5.5, 25% PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945, 0.97929
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979291
ReflectionResolution: 2.3→39.77 Å / Num. all: 10719 / Num. obs: 10719 / % possible obs: 93.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rsym value: 0.093 / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
ARP/wARPmodel building
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.3→39.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.913 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.239
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23623 534 4.7 %RANDOM
Rwork0.17374 ---
obs0.17665 10719 93.96 %-
all-10719 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.975 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å21.9 Å2
2---2.11 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 64 106 1916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221826
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.482.0022448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0315215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39722.588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87215320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3921524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021355
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2792
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21222
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3650.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.731.51126
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67721727
X-RAY DIFFRACTIONr_scbond_it3.1183786
X-RAY DIFFRACTIONr_scangle_it4.4694.5721
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 29 -
Rwork0.199 532 -
obs--64.71 %
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)
12.4577-0.36471.61155.3183-5.247114.96520.2180.0830.30010.24810.2269-0.0543-0.69350.3455-0.4449-0.0126-0.02260.2006-0.0434-0.05220.128225.031156.768514.3481
23.37482.6864-1.02154.269-0.0975.76210.0414-0.3986-0.32480.5065-0.1541-0.4950.03710.5890.11270.12070.0133-0.00930.11430.0570.122437.554255.686827.7475
35.6836-4.24386.10875.8679-6.53218.1106-0.12530.966-0.1222-0.4826-0.1881-0.39080.42560.60190.31340.2205-0.0460.20610.1352-0.07310.127924.976653.26244.8377
43.336-2.79711.9737.53710.43842.0104-0.1237-0.1019-0.2510.33230.28960.2939-0.45-0.0249-0.1659-0.1178-0.09530.1296-0.1191-0.0412-0.149318.871257.988514.7803
54.6601-0.6602-4.89652.82462.9110.242-0.202-0.00860.4072-0.2480.26490.4034-0.5473-0.0538-0.0629-0.0024-0.01950.0168-0.04520.0481-0.03287.680468.429110.731
66.1394-2.99813.03975.3757-2.6444.5926-0.02570.0029-0.4668-0.38280.14790.07060.5018-0.3448-0.12220.0151-0.1110.1669-0.185-0.0521-0.037116.832349.355213.4851
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 206 - 22
2X-RAY DIFFRACTION2AA21 - 9123 - 93
3X-RAY DIFFRACTION3AA92 - 11994 - 121
4X-RAY DIFFRACTION4BB5 - 287 - 30
5X-RAY DIFFRACTION5BB29 - 7231 - 74
6X-RAY DIFFRACTION6BB79 - 11981 - 121

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