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

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Basic information

Entry
Database: PDB / ID: 2zbu
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 / MAD / Resolution: 2.1 Å
AuthorsEbihara, A. / Fujimoto, Y. / Kagawa, W. / Fujikawa, N. / 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. / 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 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)118,7628
Polymers117,6934
Non-polymers1,0694
Water5,224290
1
A: Uncharacterized conserved protein
hetero molecules

A: Uncharacterized conserved protein
hetero molecules

A: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0716
Polymers88,2693
Non-polymers8023
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9630 Å2
MethodPISA
2
B: Uncharacterized conserved protein
hetero molecules

B: Uncharacterized conserved protein
hetero molecules

B: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0716
Polymers88,2693
Non-polymers8023
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 area9660 Å2
MethodPISA
3
C: Uncharacterized conserved protein
hetero molecules

C: Uncharacterized conserved protein
hetero molecules

C: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0716
Polymers88,2693
Non-polymers8023
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9710 Å2
MethodPISA
4
D: Uncharacterized conserved protein
hetero molecules

D: Uncharacterized conserved protein
hetero molecules

D: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0716
Polymers88,2693
Non-polymers8023
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.476, 120.476, 227.115
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

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Components

#1: Protein
Uncharacterized conserved protein


Mass: 29423.135 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium cacodylate pH6.5, 35% 2-ethoxyethanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9789, 0.9000, 0.9794
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 15, 2006
RadiationMonochromator: SI Double-Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.91
30.97941
ReflectionResolution: 2.1→50 Å / Num. obs: 71732 / % possible obs: 100 % / Redundancy: 5.5 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 25.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4123454.85 / 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
Rfree0.257 7208 10.1 %RANDOM
Rwork0.222 ---
obs0.222 71265 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9814 Å2 / ksol: 0.361763 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å23.48 Å20 Å2
2--2.82 Å20 Å2
3----5.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8248 0 76 290 8614
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_d23.8
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_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 1189 10 %
Rwork0.265 10708 -
obs--99.3 %
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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