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- PDB-2pzz: 2.2 A resolution crystal structure of UPF0201 protein from Methan... -

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Basic information

Entry
Database: PDB / ID: 2pzz
Title2.2 A resolution crystal structure of UPF0201 protein from Methanococcus jannaschii
ComponentsUPF0201 protein MJ1564
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / UPF0201 / MJ1564 / 10077a3 / Methanococcus jannaschii / PSI2 / NYSGXRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homologyUncharacterised protein family UPF0201 / RNA binding / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / 2-Layer Sandwich / Alpha Beta / UPF0201 protein MJ1564
Function and homology information
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsRao, K.N. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Plos One / Year: 2008
Title: UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function.
Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: UPF0201 protein MJ1564
B: UPF0201 protein MJ1564
C: UPF0201 protein MJ1564
D: UPF0201 protein MJ1564


Theoretical massNumber of molelcules
Total (without water)67,5844
Polymers67,5844
Non-polymers00
Water1,49583
1
A: UPF0201 protein MJ1564
C: UPF0201 protein MJ1564


Theoretical massNumber of molelcules
Total (without water)33,7922
Polymers33,7922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8 kcal/mol
Surface area12970 Å2
MethodPISA
2
B: UPF0201 protein MJ1564
D: UPF0201 protein MJ1564


Theoretical massNumber of molelcules
Total (without water)33,7922
Polymers33,7922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-6 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.520, 50.150, 73.820
Angle α, β, γ (deg.)70.34, 72.61, 84.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
UPF0201 protein MJ1564


Mass: 16896.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Species: Methanocaldococcus jannaschii / Strain: DSM 2661, JAL-1, JCM 10045, NBRC 100440 / Gene: MJ1564 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q58959
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Ammonium acetate, HEPES Buffer, PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2007 / Details: Mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 30128 / Num. obs: 30128 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2775 / % possible all: 90.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.2→47.23 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 120713.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 864 3 %RANDOM
Rwork0.249 ---
obs0.249 29198 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.4452 Å2 / ksol: 0.364126 e/Å3
Displacement parametersBiso mean: 46.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å26.45 Å2-1.06 Å2
2--0.49 Å2-12.28 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 0 83 3926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it2.52
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 143 3.3 %
Rwork0.295 4213 -
obs--85.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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