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- PDB-3l09: Crystal structure of Putative transcriptional regulator (JANN_22D... -

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Basic information

Entry
Database: PDB / ID: 3l09
TitleCrystal structure of Putative transcriptional regulator (JANN_22DEC04_CONTIG27_REVISED_GENE3569) from Jannaschia sp. CCS1 at 2.81 A resolution
ComponentsPutative transcriptional regulatorTranscriptional regulation
KeywordsTranscription regulator / Putative transcriptional regulator / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Alpha-Beta Plaits - #2670 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1460 / PaaX-like, N-terminal / PaaX-like protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily ...Alpha-Beta Plaits - #2670 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1460 / PaaX-like, N-terminal / PaaX-like protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesJannaschia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.81 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative transcriptional regulator (JANN_22DEC04_CONTIG27_REVISED_GENE3569) from Jannaschia sp. CCS1 at 2.81 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
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.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_conn ...database_2 / 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_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

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)116,46314
Polymers115,5024
Non-polymers96110
Water61334
1
A: Putative transcriptional regulator
B: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9434
Polymers57,7512
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-53 kcal/mol
Surface area23450 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-191 kcal/mol
Surface area45800 Å2
MethodPISA
3
C: Putative transcriptional regulator
D: Putative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,52010
Polymers57,7512
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-129 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.953, 81.722, 199.921
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Putative transcriptional regulator / Transcriptional regulation / PaaX-like protein


Mass: 28875.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia sp. (bacteria) / Strain: CCS1 / Gene: Jann_0659 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q28UN6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20.0000% polyethylene glycol 3350, 0.2500M lithium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97939,0.91162,0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 16, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.911621
30.979251
ReflectionResolution: 2.81→46.932 Å / Num. obs: 28370 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.565 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.29
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.81-2.910.7572.388282581191
2.91-3.030.6842.499862850199
3.03-3.160.4953.393822667199.5
3.16-3.330.3334.6103772887199.6
3.33-3.540.2276.2102652852199.6
3.54-3.810.1498.4102392809199.9
3.81-4.190.10310.7103962849199.8
4.19-4.790.07812.7105372893199.8
4.79-60.07912.7104342884199.5
6-46.9320.04617.9107723097197.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
BUSTER2.8.0refinement
PHENIXrefinement
SHELXphasing
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
MolProbity3beta29model building
RefinementMethod to determine structure: MAD / Resolution: 2.81→46.932 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.879 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. SULFATE MODELED ARE PRESENT IN CRYSTLLIZATION CONDITIONS. 3. RAMACHANDRAN OUTLIER (A6) IS LOCATED IN REGION OF POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1430 5.05 %RANDOM
Rwork0.199 ---
obs0.202 28332 --
Displacement parametersBiso max: 188.33 Å2 / Biso mean: 68.579 Å2 / Biso min: 15.83 Å2
Baniso -1Baniso -2Baniso -3
1-3.065 Å20 Å20 Å2
2--12.437 Å20 Å2
3----15.502 Å2
Refinement stepCycle: LAST / Resolution: 2.81→46.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7625 0 50 34 7709
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.12
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d2.43
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d17.89
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.81→2.92 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.327 123 4.49 %
Rwork0.235 2615 -
all0.239 2738 -
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)
14.3456-3.7260.33974.1684-0.140.0574-0.3089-0.1445-0.12940.42150.23830.45180.0402-0.20270.07060.00620.16440.0935-0.23520.1118-0.02275.6029-9.174983.48
25.0284-3.90081.52874.8348-1.37451.4173-0.635-0.4321-0.10491.08850.4535-0.7046-0.11850.16550.18160.13870.1497-0.1968-0.36390.02380.009653.2498-44.613594.4597
31.1465-1.35460.0054.57990.00330.22240.12640.14340.1493-0.0707-0.18920.6119-0.0155-0.10580.0628-0.22490.0199-0.0056-0.14880.04210.172116.44572.010957.7801
41.8001-1.3605-0.09713.2441-0.4130.4859-0.13520.0301-0.16160.16520.0254-0.10960.05320.12720.1098-0.15490.03950.0105-0.15490.00620.121143.9613-51.978667.2619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 254
2X-RAY DIFFRACTION2B5 - 255
3X-RAY DIFFRACTION3C3 - 255
4X-RAY DIFFRACTION4D3 - 253

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