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- PDB-2epi: Crystal Structure pf hypothetical protein MJ1052 from Methanocald... -

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Basic information

Entry
Database: PDB / ID: 2epi
TitleCrystal Structure pf hypothetical protein MJ1052 from Methanocaldococcus jannascii (Form 2)
ComponentsUPF0045 protein MJ1052
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyThiamine-binding protein / : / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / UPF0045 protein MJ1052
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure pf hypothetical protein MJ1052 from Methanocaldococcus jannascii
Authors: Mizutani, H. / Kunishima, N.
History
DepositionMar 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0045 protein MJ1052
B: UPF0045 protein MJ1052
C: UPF0045 protein MJ1052
D: UPF0045 protein MJ1052


Theoretical massNumber of molelcules
Total (without water)44,9734
Polymers44,9734
Non-polymers00
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-49 kcal/mol
Surface area15360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.780, 75.747, 54.991
Angle α, β, γ (deg.)90.00, 117.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UPF0045 protein MJ1052


Mass: 11243.202 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q58452
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7
Details: 30%(v/v) Jeffamine M-600, 0.1M HEPES, pH 7.0, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 9, 2007
RadiationMonochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 41290 / Num. obs: 41290 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.042 / Net I/σ(I): 11.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.24 / Num. unique all: 4121 / Rsym value: 0.302 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LXN

1lxn


Resolution: 1.7→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1036084.32 / 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
Rfree0.247 2026 4.9 %RANDOM
Rwork0.207 ---
all0.209 41269 --
obs0.207 41269 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9238 Å2 / ksol: 0.32183 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.05 Å20 Å21.6 Å2
2---3.65 Å20 Å2
3---8.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 0 419 3462
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.842.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 287 4.3 %
Rwork0.292 6376 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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