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- PDB-3h0n: Crystal structure of a duf1470 family protein (jann_2411) from ja... -

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Basic information

Entry
Database: PDB / ID: 3h0n
TitleCrystal structure of a duf1470 family protein (jann_2411) from jannaschia sp. ccs1 at 1.45 A resolution
Componentsuncharacterized protein DUF1470
KeywordsMETAL BINDING PROTEIN / Treble clef zinc finger / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Jann2411-like fold / Jann2411-like domain / Putative stress-induced transcription regulator / Zinc finger, CGNR / ABATE domain superfamily / Putative stress-induced transcription regulator / CGNR zinc finger / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / zf-CGNR domain-containing protein
Similarity search - Component
Biological speciesJannaschia sp. CCS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: The structure of Jann_2411 (DUF1470) from Jannaschia sp. at 1.45  resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator.
Authors: Bakolitsa, C. / Bateman, A. / Jin, K.K. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chiu, H.J. / ...Authors: Bakolitsa, C. / Bateman, A. / Jin, K.K. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Elias, Y. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Grzechnik, S.K. / Han, G.W. / Jaroszewski, L. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Kumar, A. / Marciano, D. / Morse, A.T. / Murphy, K.D. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H. / Trame, C.B. / Trout, C.V. / van den Bedem, H. / Weekes, D. / White, A. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S. / Wilson, I.A.
History
DepositionApr 9, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionApr 21, 2009ID: 2PW4
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / 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 / pdbx_struct_conn_angle ...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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: uncharacterized protein DUF1470
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,37610
Polymers20,8441
Non-polymers5319
Water4,324240
1
A: uncharacterized protein DUF1470
hetero molecules

A: uncharacterized protein DUF1470
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,75120
Polymers41,6882
Non-polymers1,06318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5220 Å2
ΔGint-91 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.750, 59.670, 57.820
Angle α, β, γ (deg.)90.000, 128.790, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein uncharacterized protein DUF1470


Mass: 20844.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia sp. CCS1 (bacteria) / Gene: Jann_2411, YP_510353.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q28PN4

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Non-polymers , 6 types, 249 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.40M sodium acetate, 0.10M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97920,0.97879
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2007 / 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
20.97921
30.978791
ReflectionResolution: 1.45→25.786 Å / Num. obs: 36254 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.251 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 14.38
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.45-1.50.2492.866836767197.1
1.5-1.560.1933.871877165199
1.56-1.630.144.771607076199.2
1.63-1.720.114676447430198.9
1.72-1.830.0858.175997268198.8
1.83-1.970.05711.275367040198.4
1.97-2.170.03516.877937091198
2.17-2.480.02621.877976951197.7
2.48-3.120.0229.180696937196.5
3.12-25.7860.01340.984256862193.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.45→25.786 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.706 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.053
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.ONE ZN ION, ONE NI ION, TWO NA IONS, THREE ACETATE IONS AND TWO GLYCEROL MOLECULES WERE MODELED. THE PRESENCE OF THE ZN AND NI ATOMS ARE SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS ABOVE AND BELOW THE NI AND ZN ABSORPTION EDGES AND GEOMETRY. 5.RESIDUES 0 AND 185 TO 187 ARE DISORDERED AND NOT MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.157 1810 5 %RANDOM
Rwork0.14 ---
obs0.141 36254 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.42 Å2 / Biso mean: 14.58 Å2 / Biso min: 3.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0.23 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.45→25.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 28 240 1678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211557
X-RAY DIFFRACTIONr_bond_other_d0.0010.021025
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9492125
X-RAY DIFFRACTIONr_angle_other_deg0.93332489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5325203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.34623.20578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00815242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3431516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
X-RAY DIFFRACTIONr_mcbond_it1.3173981
X-RAY DIFFRACTIONr_mcbond_other0.3433392
X-RAY DIFFRACTIONr_mcangle_it2.17951572
X-RAY DIFFRACTIONr_scbond_it3.5618576
X-RAY DIFFRACTIONr_scangle_it5.28811551
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 129 -
Rwork0.191 2516 -
all-2645 -
obs--98.11 %
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)
12.03420.0489-1.78231.0306-0.16922.55140.1309-0.13010.02950.0419-0.133-0.0257-0.230.1880.0022-0.0043-0.01470.0143-0.0157-0.0051-0.0404-5.40224.89120.03
20.07420.3361-0.38541.5469-1.65082.35470.0093-0.002-0.04120.1714-0.1234-0.156-0.15430.23490.11420.03980.0062-0.00790.06170.02120.03976.79317.50119.407
30.55450.0526-0.23550.0731-0.11880.4974-0.017-0.0058-0.0346-0.00680.00750.00680.00650.03720.0094-0.01350.00950.0029-0.0041-0.0047-0.0208-7.51620.05815.447
46.79837.7182-1.28819.0271-2.74616.4768-0.52660.74070.0487-0.51760.50930.101-0.28870.14840.01740.1407-0.0731-0.00960.13480.01380.0469.45742.7373.723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 59
3X-RAY DIFFRACTION3A60 - 172
4X-RAY DIFFRACTION4A173 - 184

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