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- PDB-4iwg: Crystal Structure of the Conserved Hypothetical Protein MJ0927 fr... -

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Basic information

Entry
Database: PDB / ID: 4iwg
TitleCrystal Structure of the Conserved Hypothetical Protein MJ0927 from Methanocaldococcus jannaschii (in C2221 form)
ComponentsUPF0135 protein MJ0927
KeywordsUNKNOWN FUNCTION / Nif3-like
Function / homology
Function and homology information


DNA binding / metal ion binding / cytoplasm
Similarity search - Function
DUF34/NIF3 / Duf34/NIF3 (NGG1p interacting factor 3) / DUF34/NIF3 superfamily / NIF3 (NGG1p interacting factor 3)-like / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GTP cyclohydrolase 1 type 2 homolog
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.472 Å
AuthorsKuan, S.M. / Chen, S.C. / Yang, C.S. / Chen, Y.R. / Liu, Y.H. / Chen, Y.
CitationJournal: Biomed Res Int / Year: 2014
Title: Crystal structure of a conserved hypothetical protein MJ0927 from Methanocaldococcus jannaschii reveals a novel quaternary assembly in the Nif3 family.
Authors: Chen, S.C. / Huang, C.H. / Yang, C.S. / Kuan, S.M. / Lin, C.T. / Chou, S.H. / Chen, Y.
History
DepositionJan 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: UPF0135 protein MJ0927
B: UPF0135 protein MJ0927
C: UPF0135 protein MJ0927


Theoretical massNumber of molelcules
Total (without water)85,4123
Polymers85,4123
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UPF0135 protein MJ0927
B: UPF0135 protein MJ0927
C: UPF0135 protein MJ0927

A: UPF0135 protein MJ0927
B: UPF0135 protein MJ0927
C: UPF0135 protein MJ0927


Theoretical massNumber of molelcules
Total (without water)170,8246
Polymers170,8246
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area14830 Å2
ΔGint-29 kcal/mol
Surface area57800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.209, 172.939, 147.422
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 UPF0135 protein MJ0927


Mass: 28470.748 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ0927 / Plasmid: pET24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58337
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M (NH4)2SO4, 0.3M sodium formate, 0.1M sodium acetate, 3% PGA-LM, 20% MPD , pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97921, 0.97938, 0.96414
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979381
30.964141
ReflectionResolution: 2.47→30 Å / Num. all: 37826 / Num. obs: 37448 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.47→2.56 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3692 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.472→24.978 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 1869 5 %RANDOM
Rwork0.1812 ---
obs0.184 37404 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.472→24.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5796 0 0 126 5922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075901
X-RAY DIFFRACTIONf_angle_d1.0857953
X-RAY DIFFRACTIONf_dihedral_angle_d15.4072208
X-RAY DIFFRACTIONf_chiral_restr0.074918
X-RAY DIFFRACTIONf_plane_restr0.0051002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.472-2.53920.35811330.2419268999
2.5392-2.61380.30891320.23632692100
2.6138-2.69810.32551530.22872680100
2.6981-2.79440.30321630.23392705100
2.7944-2.90610.27911460.21582704100
2.9061-3.03820.26611320.22172701100
3.0382-3.1980.31511270.22692760100
3.198-3.39790.26861330.20922741100
3.3979-3.65960.27411430.2082725100
3.6596-4.02640.21631420.17932740100
4.0264-4.60590.19271520.14042741100
4.6059-5.7910.19141490.15512788100
5.791-24.97890.1891640.13842869100

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