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- PDB-2fcj: Structure of small TOPRIM domain protein from Bacillus stearother... -

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Basic information

Entry
Database: PDB / ID: 2fcj
TitleStructure of small TOPRIM domain protein from Bacillus stearothermophilus.
Componentssmall TOPRIM domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / TOPRIM domain / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


ribonuclease M5 activity / rRNA processing / metal ion binding
Similarity search - Function
Ribonuclease M5-like, TOPRIM domain / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 / Dna Topoisomerase Vi A Subunit; Chain: A, domain 2 - #10 / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hypothetical conserved protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsRezacova, P. / Chen, Y. / Borek, D. / Collart, F. / Joachimiak, A. / Otwinowski, Z. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2008
Title: Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus.
Authors: Rezacova, P. / Borek, D. / Moy, S.F. / Joachimiak, A. / Otwinowski, Z.
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THERE WAS NO SUITABLE SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: small TOPRIM domain protein
B: small TOPRIM domain protein
C: small TOPRIM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7288
Polymers41,1563
Non-polymers5725
Water7,080393
1
A: small TOPRIM domain protein


Theoretical massNumber of molelcules
Total (without water)13,7191
Polymers13,7191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: small TOPRIM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9033
Polymers13,7191
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: small TOPRIM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1064
Polymers13,7191
Non-polymers3873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: small TOPRIM domain protein
hetero molecules

C: small TOPRIM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0097
Polymers27,4372
Non-polymers5725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area1990 Å2
ΔGint-31 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.617, 72.720, 116.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 3 - 113 / Label seq-ID: 3 - 113

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein small TOPRIM domain protein


Mass: 13718.728 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP2199 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KVJ9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH6.0; 26% PEG3350; 0.2M Ammonium Sulfate; 18% glycerol; protein concentration 3.5mg/ml; micro-seeding, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 77810 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 15.7 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.032 / Net I/σ(I): 76.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 3640 / Rsym value: 0.536 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.386 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21399 1538 2 %RANDOM
Rwork0.1919 ---
obs0.19238 75438 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 34 393 3219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223001
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.984070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49722.848158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16415547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9111541
X-RAY DIFFRACTIONr_chiral_restr0.0850.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022276
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.31411
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.52117
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.5550
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.3105
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.5104
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.69121850
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34532911
X-RAY DIFFRACTIONr_scbond_it2.2921276
X-RAY DIFFRACTIONr_scangle_it3.19831157
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A419medium positional0.460.5
2B419medium positional0.310.5
3C419medium positional0.480.5
1A377loose positional15
2B377loose positional0.975
3C377loose positional1.165
1A419medium thermal2.772
2B419medium thermal1.792
3C419medium thermal2.62
1A377loose thermal3.3410
2B377loose thermal2.5510
3C377loose thermal2.9810
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 95 -
Rwork0.276 5303 -
obs--96.1 %

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