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- PDB-2fcl: Crystal structure of a putative nucleotidyltransferase (tm1012) f... -

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Basic information

Entry
Database: PDB / ID: 2fcl
TitleCrystal structure of a putative nucleotidyltransferase (tm1012) from Thermotoga maritima at 1.35 A resolution
Componentshypothetical protein TM1012Hypothesis
KeywordsTRANSFERASE / PUTATIVE NUCLEOTIDYLTRANSFERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyBeta Polymerase; domain 2 - #40 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta / Unknown ligand / : / Uncharacterized protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (tm1012) from Thermotoga maritima at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TM1012
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6184
Polymers20,4941
Non-polymers1243
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.769, 36.382, 39.785
Angle α, β, γ (deg.)73.690, 85.510, 78.970
Int Tables number1
Space group name H-MP1

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Components

#1: Protein hypothetical protein TM1012 / Hypothesis


Mass: 20493.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1012 / Production host: Escherichia coli (E. coli) / References: GenBank: 4981552, UniProt: Q9X0A5*PLUS
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 43.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.6
Details: 15.0% Glycerol, 0.17M NH4OAc, 25.5% PEG-4000, 0.1M Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979454 / Wavelength: 0.979454 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2005 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979454 Å / Relative weight: 1
ReflectionResolution: 1.2→25.88 Å / Num. obs: 39827 / % possible obs: 73.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.034 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsRsym value% possible all
1.2-1.2320.1465.714047090.14617.6
1.23-1.2620.1296.7200610120.12925.9
1.26-1.320.1087.6268713600.10835.5
1.3-1.3420.0918.7349317600.09147.6
1.34-1.3920.07710443222360.07763.4
1.39-1.4320.06411607730640.06488.3
1.43-1.4920.05312.9609030650.05391.8
1.49-1.5520.04615.1584629480.04692
1.55-1.6220.03917.5560328240.03991.8
1.62-1.720.03619539927180.03692.4
1.7-1.7920.03320.9513625880.03392.5
1.79-1.920.03123493924870.03193
1.9-2.0320.03525456922670.03591.9
2.03-2.192.30.03427.5485821590.03492.9
2.19-2.42.50.03529.5504720330.03596.4
2.4-2.683.10.04633.1587618850.04696.9
2.68-3.13.60.03936.4592216540.03997.6
3.1-3.793.70.0337.5514913890.0397.4
3.79-5.374.40.03141.8479310990.03198.6
5.37-25.884.10.03140.223505700.03194.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ewr

2ewr


Resolution: 1.2→24.28 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.958 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THE NOMINAL RESOLUTION IS 1.35 A WITH 4948 OBSERVED REFLECTIONS BETWEEN 1.35-1.20 (33.6% COMPLETE FOR THIS SHELL) INCLUDED IN THE ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) THE NOMINAL RESOLUTION IS 1.35 A WITH 4948 OBSERVED REFLECTIONS BETWEEN 1.35-1.20 (33.6% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. (3) DENSITY NEAR RESIDUES 116 AND 129 WAS MODELED AS AN UNKNOWN LIGAND (UNL).
RfactorNum. reflection% reflectionSelection details
Rfree0.17 2028 5.1 %RANDOM
Rwork0.14 ---
obs0.142 37613 74.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.634 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20.31 Å2-0.17 Å2
2---0.24 Å20.22 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.2→24.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 14 261 1583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221412
X-RAY DIFFRACTIONr_bond_other_d0.0020.021350
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9811914
X-RAY DIFFRACTIONr_angle_other_deg0.78533125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50424.11868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99415.181277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.171510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
X-RAY DIFFRACTIONr_nbd_refined0.2370.2271
X-RAY DIFFRACTIONr_nbd_other0.1890.21439
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2691
X-RAY DIFFRACTIONr_nbtor_other0.0820.2875
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0780.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.223
X-RAY DIFFRACTIONr_mcbond_it2.1883853
X-RAY DIFFRACTIONr_mcbond_other1.4453336
X-RAY DIFFRACTIONr_mcangle_it2.87251345
X-RAY DIFFRACTIONr_scbond_it3.7498638
X-RAY DIFFRACTIONr_scangle_it4.99211564
X-RAY DIFFRACTIONr_rigid_bond_restr2.00231485
X-RAY DIFFRACTIONr_sphericity_bonded4.33631372
LS refinement shellResolution: 1.201→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 35 -
Rwork0.143 507 -
obs--18.39 %

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