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- PDB-3mvu: Crystal structure of a TenA family transcription regulator (TM104... -

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Basic information

Entry
Database: PDB / ID: 3mvu
TitleCrystal structure of a TenA family transcription regulator (TM1040_3656) from SILICIBACTER SP. TM1040 at 1.80 A resolution
ComponentsTenA family transcriptional regulator
Keywordstranscription regulator / TENA/THI-4/PQQC family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / TRANSCRIPTION
Function / homology
Function and homology information


aminopyrimidine aminohydrolase / thiaminase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / cytosol
Similarity search - Function
Thiaminase II / : / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / Aminopyrimidine aminohydrolase
Similarity search - Component
Biological speciesRuegeria sp. TM1040 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a TenA family transcription regulator (TM1040_3656) from SILICIBACTER SP. TM1040 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TenA family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,05415
Polymers25,2051
Non-polymers84914
Water1,928107
1
A: TenA family transcriptional regulator
hetero molecules

A: TenA family transcriptional regulator
hetero molecules

A: TenA family transcriptional regulator
hetero molecules

A: TenA family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,21560
Polymers100,8184
Non-polymers3,39756
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area7550 Å2
ΔGint-51.8 kcal/mol
Surface area32950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.315, 65.315, 107.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
DetailsLIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein TenA family transcriptional regulator


Mass: 25204.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria sp. TM1040 (bacteria) / Gene: TM1040_3656 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GL43
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2000M magnesium acetate, 22.0000% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.0, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97935,0.97882
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 12, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979351
30.978821
ReflectionResolution: 1.8→29.21 Å / Num. obs: 22224 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.857.20.6661.21151916100.666100
1.85-1.97.20.5481.41120815570.548100
1.9-1.957.10.4171.81086315200.417100
1.95-2.017.20.3212.41071214960.321100
2.01-2.087.20.2433.11020814190.243100
2.08-2.157.20.1874.11011214130.187100
2.15-2.237.20.1415.3966913510.141100
2.23-2.327.10.126.2939313160.12100
2.32-2.437.10.1036.9889012480.103100
2.43-2.557.10.0877.7846411840.087100
2.55-2.687.10.0838.3813611470.083100
2.68-2.857.10.0788.4775910980.078100
2.85-3.047.10.0748.4720510180.074100
3.04-3.2970.0611068719770.061100
3.29-3.670.0512.361708840.05100
3.6-4.0270.03915.357258230.039100
4.02-4.656.80.04214.350107350.042100
4.65-5.696.70.04513.441176180.045100
5.69-8.056.30.03915.832265110.03999.9
8.05-29.215.40.03318.416002990.03395.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0059refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.476 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET- ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. CHLORIDE (CL) ION, IMIDAZOLE (IMD), AND ETHYLENE GLYCOL (EDO) MOLECULES FROM THE PURIFICATION/CRYOPROTECTION SOLUTION ARE MODELED. 6. RESIDUES 84-91 HAVE POOR ELECTRON DENSITY SUPPORT.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 1132 5.1 %RANDOM
Rwork0.165 ---
obs0.165 22179 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 129.65 Å2 / Biso mean: 38.752 Å2 / Biso min: 18.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 54 107 1883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211855
X-RAY DIFFRACTIONr_bond_other_d0.0010.021272
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9582502
X-RAY DIFFRACTIONr_angle_other_deg0.90833059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7425238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.60522.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84615284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.221515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02419
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 77 -
Rwork0.218 1530 -
all-1607 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 26.559 Å / Origin y: 16.384 Å / Origin z: 40.083 Å
111213212223313233
T0.1155 Å2-0.0212 Å2-0.0185 Å2-0.047 Å2-0.005 Å2--0.028 Å2
L1.473 °20.3749 °20.1605 °2-1.5292 °20.112 °2--1.6119 °2
S0.0063 Å °0.2141 Å °-0.0697 Å °-0.2415 Å °0.0987 Å °0.0077 Å °0.1394 Å °-0.0496 Å °-0.1051 Å °

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