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- PDB-3whp: Crystal structure of the C-terminal domain of Themus thermophilus... -

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Basic information

Entry
Database: PDB / ID: 3whp
TitleCrystal structure of the C-terminal domain of Themus thermophilus LitR in complex with cobalamin
ComponentsProbable transcriptional regulator
KeywordsGENE REGULATION / B12-binding domain / Rossmann fold / Four helix bundle / Transcriptional Regulator / Cobalamin
Function / homology
Function and homology information


cobalamin binding / DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
Methionine synthase domain / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance ...Methionine synthase domain / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / Cobalamin-binding domain superfamily / MerR-type HTH domain / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Putative DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COBALAMIN / Probable transcriptional regulator
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.52 Å
AuthorsAgari, Y. / Takano, H. / Beppu, T. / Ueda, K. / Shinkai, A.
CitationJournal: To be Published
Title: Crystal structure of the C-terminal domain of Themus thermophilus LitR in complex with cobalamin
Authors: Agari, Y. / Takano, H. / Beppu, T. / Ueda, K. / Shinkai, A.
History
DepositionAug 30, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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

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Assembly

Deposited unit
A: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8942
Polymers31,5631
Non-polymers1,3301
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.366, 95.366, 50.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Probable transcriptional regulator / Transcriptional Regulator LitR


Mass: 31563.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: litR, TT_P0056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q746J7
#2: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE C19 (B12 A 800) IN THIS COORDINATES HAS PLANAR CONFIGURATION WITH UNKNOWN REASON.

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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: 1.81 Å3/Da / Density % sol: 32.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M Phosphate-citrate, 5% PEG 1000, 35%-40% Ethanol, 0.18-0.36M Mg sulfate, 0.01-0.02M Na acetate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.00, 1.6042, 1.6083, 1.5600
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 27, 2012
RadiationMonochromator: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.60421
31.60831
41.561
ReflectionResolution: 2.52→50 Å / Num. obs: 8257 / % possible obs: 99.8 % / Redundancy: 13 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 51.4
Reflection shellResolution: 2.52→2.58 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 7.8 / Num. unique all: 559 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.52→32.54 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2368756.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 875 10.6 %RANDOM
Rwork0.224 ---
all0.226 8230 --
obs0.224 8230 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.1639 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 59.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.16 Å20 Å20 Å2
2--4.16 Å20 Å2
3----8.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.52→32.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 91 27 1564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.171.5
X-RAY DIFFRACTIONc_mcangle_it6.792
X-RAY DIFFRACTIONc_scbond_it8.552
X-RAY DIFFRACTIONc_scangle_it11.112.5
LS refinement shellResolution: 2.52→2.68 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 141 10.8 %
Rwork0.252 1168 -
obs-1309 99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6B12_param.txtB12_top.txt

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