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- PDB-2b33: CRYSTAL STRUCTURE OF A PUTATIVE ENDORIBONUCLEASE (TM0215) FROM TH... -

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Basic information

Entry
Database: PDB / ID: 2b33
TitleCRYSTAL STRUCTURE OF A PUTATIVE ENDORIBONUCLEASE (TM0215) FROM THERMOTOGA MARITIMA MSB8 AT 2.30 A RESOLUTION
Componentsprotein synthesis inhibitor, putative
KeywordsHYDROLASE / PROTEIN SYNTHESIS INHIBITOR / PUTATIVE ENDORIBONUCLEASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


organonitrogen compound catabolic process / deaminase activity / metal ion binding / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein synthesis inhibitor, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Protein synthesis inhibitor, putative (tm0215) from THERMOTOGA MARITIMA at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein synthesis inhibitor, putative
B: protein synthesis inhibitor, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7186
Polymers31,4922
Non-polymers2264
Water1,44180
1
A: protein synthesis inhibitor, putative
hetero molecules

A: protein synthesis inhibitor, putative
hetero molecules

A: protein synthesis inhibitor, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6109
Polymers47,2383
Non-polymers3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6260 Å2
ΔGint-31 kcal/mol
Surface area14830 Å2
MethodPISA, PQS
2
B: protein synthesis inhibitor, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8483
Polymers15,7461
Non-polymers1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: protein synthesis inhibitor, putative
hetero molecules

B: protein synthesis inhibitor, putative
hetero molecules

B: protein synthesis inhibitor, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5449
Polymers47,2383
Non-polymers3066
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.280, 53.280, 228.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILE1AA1 - 3513 - 47
21LYSLYSILEILE1BB2 - 3514 - 47
32ASPASPLYSLYS2AA36 - 5048 - 62
42ASPASPLYSLYS2BB36 - 5048 - 62
53THRTHRASPASP1AA51 - 8363 - 95
63THRTHRASPASP1BB51 - 8363 - 95
74TYRTYRGLUGLU2AA84 - 11696 - 128
84TYRTYRGLUGLU2BB84 - 11696 - 128
95ILEILEGLYGLY1AA117 - 127129 - 139
105ILEILEGLYGLY1BB117 - 127129 - 139

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Components

#1: Protein protein synthesis inhibitor, putative /


Mass: 15745.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0215 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WY58
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.98 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.3
Details: 0.2 M Ca Acetate, 20.0% PEG 3350, No Buffer, pH 7.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.95372
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2005 / Details: PAIR OF BIMORPH KIRKPATRICK-BAEZ MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.12→26.64 Å / Num. obs: 13161 / % possible obs: 80.9 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.218 / Net I/σ(I): 5.27
Reflection shell

Rmerge(I) obs: 0.901 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)% possible obs (%)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. unique obs
2.12-2.267.31.151.7633481964
2.2-2.2868.11.9630241707
2.28-2.3969.82.3135932040
2.39-2.5170.72.433601877
2.51-2.6770.92.9636772041
2.67-2.8889.23.4462182480
2.88-3.1690.64.7661742440
3.16-3.62936.8465982605
3.62-4.5595.19.7165972618
4.5594.612.2967992682

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1qahA

Resolution: 2.3→26.64 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.89 / SU B: 20.53 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A CALCIUM CATION FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED INTO THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.261 504 4.9 %RANDOM
Rwork0.199 ---
all0.202 ---
obs-9833 96.07 %-
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: 34.829 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å2-1.33 Å20 Å2
2---2.66 Å20 Å2
3---3.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 13 80 2030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221979
X-RAY DIFFRACTIONr_bond_other_d0.0020.021849
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9652678
X-RAY DIFFRACTIONr_angle_other_deg0.99434276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9225251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.11824.36887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.41415328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8411513
X-RAY DIFFRACTIONr_chiral_restr0.0810.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022205
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
X-RAY DIFFRACTIONr_nbd_refined0.1610.3340
X-RAY DIFFRACTIONr_nbd_other0.140.31855
X-RAY DIFFRACTIONr_nbtor_refined0.1650.5944
X-RAY DIFFRACTIONr_nbtor_other0.0810.51046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.5132
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1150.370
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.515
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2060.51
X-RAY DIFFRACTIONr_mcbond_it0.85831312
X-RAY DIFFRACTIONr_mcbond_other0.193516
X-RAY DIFFRACTIONr_mcangle_it1.29552036
X-RAY DIFFRACTIONr_scbond_it2.7478767
X-RAY DIFFRACTIONr_scangle_it4.01311642
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
1384tight positional0.020.05
462medium positional0.440.5
1384tight thermal0.060.5
462medium thermal0.442
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 37 -
Rwork0.271 680 -
obs--90.87 %
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)
12.6884-0.2547-1.09413.36890.20725.7627-0.04790.3420.1955-0.3142-0.1784-0.3309-0.40250.14490.2263-0.0038-0.0386-0.0344-0.06830.0855-0.11744.01112.5375.716
23.25540.00010.49793.68411.58093.7580.0063-0.117-0.24250.195-0.0372-0.15950.0238-0.04910.0309-0.1155-0.01290.0183-0.15730.0213-0.2719-0.21417.502110.32
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 12713 - 139
2X-RAY DIFFRACTION2BB2 - 12714 - 139

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