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- PDB-2zbv: Crystal structure of uncharacterized conserved protein from Therm... -

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Basic information

Entry
Database: PDB / ID: 2zbv
TitleCrystal structure of uncharacterized conserved protein from Thermotoga maritima
ComponentsUncharacterized conserved protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Uncharacterized conserved protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase N-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 ...Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase N-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / Adenosyl-chloride synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsEbihara, A. / Fujimoto, Y. / Kagawa, W. / Fujikawa, N. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized conserved protein from Thermotoga maritima
Authors: Ebihara, A. / Fujimoto, Y. / Kagawa, W. / Fujikawa, N. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Yokoyama, S. / Kuramitsu, S.
History
DepositionOct 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized conserved protein
B: Uncharacterized conserved protein
C: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0716
Polymers88,2693
Non-polymers8023
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.200, 136.697, 186.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Uncharacterized conserved protein


Mass: 29423.135 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: Q9WZC8
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1M Sodium cacodylate pH 6.3, 31% 2-ethoxyethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 58169 / % possible obs: 98.4 % / Redundancy: 12.6 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 34.1
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.5 / % possible all: 86.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YYP

2yyp
PDB Unreleased entry


Resolution: 2.05→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3423514.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 5906 10.2 %RANDOM
Rwork0.214 ---
obs0.214 58018 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7395 Å2 / ksol: 0.353184 e/Å3
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å20 Å2
2--9.06 Å20 Å2
3----7.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6117 0 57 233 6407
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 884 10.1 %
Rwork0.252 7911 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3adn_xplor.paramadn_xplor.top

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