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- PDB-2p5d: Crystal structure of MJECL36 from Methanocaldococcus jannaschii D... -

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Basic information

Entry
Database: PDB / ID: 2p5d
TitleCrystal structure of MJECL36 from Methanocaldococcus jannaschii DSM 2661
ComponentsUPF0310 protein MJECL36
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Methanocaldococcus jannaschii / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyUncharacterised protein family UPF0310 / EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta / UPF0310 protein MJECL36
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of MJECL36 from Methanocaldococcus jannaschii DSM 2661
Authors: Sugahara, M. / Kunishima, N.
History
DepositionMar 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0310 protein MJECL36


Theoretical massNumber of molelcules
Total (without water)17,5751
Polymers17,5751
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.866, 65.088, 71.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is monomer in the asymmetric.

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Components

#1: Protein UPF0310 protein MJECL36


Mass: 17574.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q60257
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 291 K / Method: oil microbatch / pH: 5.5
Details: 27.5% PEG 4000, 0.1M Acetate-NaOH, 10% Dioxane, pH 5.5, oil microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 16540 / Num. obs: 16540 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 19.38 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.037 / Net I/σ(I): 15.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1625 / Rsym value: 0.176 / % possible all: 100

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Processing

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

1wmm


Resolution: 1.7→19.25 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 828 -RANDOM
Rwork0.216 ---
obs0.216 16490 99.8 %-
all-16490 --
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2--3.6 Å20 Å2
3----4.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 0 194 1415
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.279 85 -
Rwork0.257 --
obs-1516 98.9 %

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