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- PDB-1o3u: Crystal structure of an hepn domain protein (tm0613) from thermot... -

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Basic information

Entry
Database: PDB / ID: 1o3u
TitleCrystal structure of an hepn domain protein (tm0613) from thermotoga maritima at 1.75 A resolution
Componentsconserved hypothetical protein TM0613
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyHEPN domain profile. / Higher Eukarytoes and Prokaryotes Nucleotide-binding domain / HEPN domain / HEPN domain / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / HEPN domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: PROTEINS / Year: 2004
Title: Crystal structure of an HEPN domain protein (TM0613) from Thermotoga maritima at 1.75 A resolution.
Authors: Erlandsen, H. / Canaves, J.M. / Elsliger, M.A. / von Delft, F. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Jaroszewski, L. / Klock, H. ...Authors: Erlandsen, H. / Canaves, J.M. / Elsliger, M.A. / von Delft, F. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Robb, A. / Quijano, K. / Schwarzenbacher, R. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionMar 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The biological unit was adjudged a dimer based on a considerable hydrophobic interface generated by crystallographic symmetry.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein TM0613


Theoretical massNumber of molelcules
Total (without water)15,6221
Polymers15,6221
Non-polymers00
Water2,306128
1
A: conserved hypothetical protein TM0613

A: conserved hypothetical protein TM0613


Theoretical massNumber of molelcules
Total (without water)31,2452
Polymers31,2452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)57.922, 57.922, 63.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein conserved hypothetical protein TM0613


Mass: 15622.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0613 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ82
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 1.74 Å3/Da / Density % sol: 28.84 %
Crystal growTemperature: 293 K / pH: 8
Details: 10% PEG 8000; Imidazole pH 8.0; 0.2 M Ca(Ac)2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 8.00
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
410 %(w/v)PEG80001reservoir
5200 mMcalcium acetate1reservoir
6100 mMimidazole1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97910, 0.97930, 0.91840
DetectorType: ADSC / Detector: CCD / Date: Dec 11, 2002
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
30.91841
ReflectionResolution: 1.75→25.904 Å / Num. obs: 10935 / % possible obs: 95.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 27.98 Å2 / Rsym value: 0.076 / Net I/σ(I): 16.5
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.417 / % possible all: 72.3
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 43.03 Å / Num. obs: 10976 / Num. measured all: 55732 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 72.3 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
RESOLVEmodel building
SOLVEphasing
REFMACrefinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→25.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.266 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1079 9.9 %RANDOM
Rwork0.179 ---
obs0.185 9855 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 0 128 1091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021993
X-RAY DIFFRACTIONr_bond_other_d0.0020.02859
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9321338
X-RAY DIFFRACTIONr_angle_other_deg0.78731999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8465118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3723.88954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71215168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.45157
X-RAY DIFFRACTIONr_chiral_restr0.0760.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021117
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02212
X-RAY DIFFRACTIONr_nbd_refined0.2110.2246
X-RAY DIFFRACTIONr_nbd_other0.2350.2956
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.2578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9361.5599
X-RAY DIFFRACTIONr_mcangle_it1.8132950
X-RAY DIFFRACTIONr_scbond_it3.0513394
X-RAY DIFFRACTIONr_scangle_it5.1624.5388
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 53
Rwork0.242 524
Refinement TLS params.Method: refined / Origin x: 6.772 Å / Origin y: 9.138 Å / Origin z: 19.047 Å
111213212223313233
T0.0183 Å2-0.0181 Å2-0.0062 Å2-0.0104 Å20.006 Å2---0.0288 Å2
L1.1148 °2-0.7699 °2-0.0669 °2-1.6545 °20.6988 °2--0.5058 °2
S0.037 Å °0.1649 Å °0.0367 Å °-0.2173 Å °0.0346 Å °-0.0922 Å °-0.1733 Å °-0.0567 Å °-0.0716 Å °
Software
*PLUS
Name: REFMAC / Version: 5.1.995 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 10934 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.26
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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