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- PDB-2fzt: CRYSTAL STRUCTURE OF a putative nucleic acid binding protein (TM0... -

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Basic information

Entry
Database: PDB / ID: 2fzt
TitleCRYSTAL STRUCTURE OF a putative nucleic acid binding protein (TM0693) FROM THERMOTOGA MARITIMA MSB8 AT 2.05 A RESOLUTION
Componentshypothetical protein TM0693
KeywordsGENE REGULATION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / TM0693-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / metal ion binding / ISOPROPYL ALCOHOL / : / Flagellar protein FliT
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (tm0693) from THERMOTOGA MARITIMA at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TM0693
B: hypothetical protein TM0693
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1103
Polymers19,0492
Non-polymers601
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-23 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.630, 27.430, 65.380
Angle α, β, γ (deg.)90.000, 102.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 1 - 77 / Label seq-ID: 2 - 78

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein hypothetical protein TM0693


Mass: 9524.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0693 / Plasmid: MH1TEV / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: GenBank: 4981216, UniProt: Q9WZF7*PLUS
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 10.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797, 0.9999
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.99991
ReflectionResolution: 2.05→50 Å / Num. obs: 11175 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.098 / Χ2: 0.983 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2% possible all
2.05-2.11003.60.5148090.99100
2.1-2.1699.93.70.387680.939
2.16-2.221003.70.3167681.027
2.22-2.291003.70.2788170.969
2.29-2.381003.70.2267670.931
2.38-2.471003.70.2018050.981
2.47-2.581003.70.1697821.044
2.58-2.721003.70.1567960.975
2.72-2.891003.70.1167771.037
2.89-3.1199.93.70.0928131.008
3.11-3.431003.70.0767980.993
3.43-3.921003.60.0678170.937
3.92-4.941003.60.0528000.984
4.94-5099.53.40.0478580.941

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SHELXphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→21.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU B: 10.085 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.193
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2.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.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 532 4.8 %RANDOM
Rwork0.194 ---
all0.197 ---
obs0.197 11154 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.138 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å2-0.8 Å2
2--0.16 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.05→21.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1263 0 4 140 1407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221274
X-RAY DIFFRACTIONr_bond_other_d0.0010.021275
X-RAY DIFFRACTIONr_angle_refined_deg1.2262.0271697
X-RAY DIFFRACTIONr_angle_other_deg0.83332966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7925157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.75124.90955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78915294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9591512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
X-RAY DIFFRACTIONr_nbd_refined0.2110.2294
X-RAY DIFFRACTIONr_nbd_other0.1680.21244
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2631
X-RAY DIFFRACTIONr_nbtor_other0.0810.2771
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.28
X-RAY DIFFRACTIONr_mcbond_it2.1983899
X-RAY DIFFRACTIONr_mcbond_other0.5693320
X-RAY DIFFRACTIONr_mcangle_it2.69651274
X-RAY DIFFRACTIONr_scbond_it5.4548503
X-RAY DIFFRACTIONr_scangle_it7.67411422
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
457MEDIUM POSITIONAL0.20.5
745LOOSE POSITIONAL0.655
457MEDIUM THERMAL0.892
745LOOSE THERMAL2.3110
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 37 -
Rwork0.221 807 -
obs-844 99.88 %
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)
11.61430.57951.50211.34411.66875.22840.00850.150.1184-0.0283-0.01050.03640.09940.12920.002-0.121200.0288-0.12020.0338-0.063716.07171.99537.3357
22.28911.28012.02771.50471.27423.6101-0.06080.0638-0.0077-0.0447-0.0384-0.0115-0.14550.12150.0992-0.08840.01110.027-0.08680.005-0.056928.439312.765530.0868
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 782 - 79
22BB0 - 781 - 79

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