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- PDB-2g42: Crystal structure of a putative nucleic acid binding protein (tm0... -

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Basic information

Entry
Database: PDB / ID: 2g42
TitleCrystal structure of a putative nucleic acid binding protein (tm0693) from thermotoga maritima at 2.28 A resolution
Componentshypothetical protein TM_0693Hypothesis
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 / Flagellar protein FliT
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (tm0693) from Thermotoga maritima at 2.28 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_leaving_atom_flag / _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.ptnr1_label_seq_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_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
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 TM_0693
B: hypothetical protein TM_0693
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0903
Polymers19,0492
Non-polymers401
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-33 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.174, 26.761, 73.221
Angle α, β, γ (deg.)90.000, 97.230, 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 label comp-ID: MSE / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 1 - 74 / Label seq-ID: 2 - 75

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 TM_0693 / Hypothesis


Mass: 9524.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm0693 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZF7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.18 Å3/Da / Density % sol: 43.23 %
Description: AFTER THE INITIAL TRACE, A MODEL OF TM0693 IN A DIFFERENT CELL (PDB ENTRY 2FZT) WAS USED TO FACILITATE COMPLETION OF THE MODEL.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.1
Details: 0.2M CaCl2, 20.0% PEG-3350, No Buffer, pH 5.1, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.28→40.859 Å / Num. obs: 7150 / % possible obs: 94.9 % / Redundancy: 6.777 % / Biso Wilson estimate: 42.374 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.28-2.353.3980.4752.73133438566.4
2.35-2.440.4524361063084.8
2.44-2.560.3925481474294.4
2.56-2.690.3246.4500068995.4
2.69-2.860.2199.1546173497.1
2.86-3.080.15811.6553274297.9
3.08-3.390.10416.4552374698.5
3.39-3.870.07321.3540174098.4
3.870.05525.8555776698.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→40.8 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.565 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.438 / ESU R Free: 0.26
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
Rfree0.251 330 4.6 %RANDOM
Rwork0.203 ---
obs0.206 7134 94.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.727 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å2-0.14 Å2
2--1.32 Å20 Å2
3----3.65 Å2
Refinement stepCycle: LAST / Resolution: 2.28→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 1 72 1309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221240
X-RAY DIFFRACTIONr_bond_other_d0.0010.021240
X-RAY DIFFRACTIONr_angle_refined_deg0.922.0191655
X-RAY DIFFRACTIONr_angle_other_deg0.71332866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4515155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24524.61552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61315273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5121512
X-RAY DIFFRACTIONr_chiral_restr0.0520.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
X-RAY DIFFRACTIONr_nbd_refined0.1880.2315
X-RAY DIFFRACTIONr_nbd_other0.1580.21240
X-RAY DIFFRACTIONr_nbtor_refined0.1620.2616
X-RAY DIFFRACTIONr_nbtor_other0.080.2791
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.24
X-RAY DIFFRACTIONr_mcbond_it1.2423822
X-RAY DIFFRACTIONr_mcbond_other0.2853320
X-RAY DIFFRACTIONr_mcangle_it1.97451257
X-RAY DIFFRACTIONr_scbond_it3.8058468
X-RAY DIFFRACTIONr_scangle_it5.62811398
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
442MEDIUM POSITIONAL0.20.5
698LOOSE POSITIONAL0.95
442MEDIUM THERMAL0.552
698LOOSE THERMAL1.9210
LS refinement shellResolution: 2.281→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 22 -
Rwork0.225 339 -
obs-361 65.4 %
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)
11.9731-1.34881.81412.3223-3.697218.14210.13190.31890.0609-0.271-0.210.0179-0.2529-0.16110.0782-0.2332-0.04240.0129-0.20090.0123-0.1256-11.6951-3.179912.7319
22.42820.3523-1.10622.8019-4.624811.0353-0.2174-0.3697-0.0473-0.18480.3150.15710.7017-0.3202-0.0976-0.1887-0.0417-0.0399-0.18010.0208-0.1298-15.216-14.112338.8028
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 781 - 79
22BB0 - 771 - 78

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