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- PDB-3lme: Structure of probable translation initiation inhibitor from (RPA2... -

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Basic information

Entry
Database: PDB / ID: 3lme
TitleStructure of probable translation initiation inhibitor from (RPA2473) from Rhodopseudomonas palustris
ComponentsPossible translation initiation inhibitor
KeywordsTRANSLATION / structural genomics / translation initiation inhibitor / RPA2473 / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyYjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / Possible translation initiation inhibitor
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of probable translation initiation inhibitor from (RPA2473) from Rhodopseudomonas palustris
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Possible translation initiation inhibitor
B: Possible translation initiation inhibitor
C: Possible translation initiation inhibitor
D: Possible translation initiation inhibitor
E: Possible translation initiation inhibitor
F: Possible translation initiation inhibitor
G: Possible translation initiation inhibitor
H: Possible translation initiation inhibitor
I: Possible translation initiation inhibitor
J: Possible translation initiation inhibitor
K: Possible translation initiation inhibitor
L: Possible translation initiation inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,82826
Polymers179,48312
Non-polymers1,34514
Water45025
1
A: Possible translation initiation inhibitor
B: Possible translation initiation inhibitor
C: Possible translation initiation inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1596
Polymers44,8713
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-97 kcal/mol
Surface area14590 Å2
MethodPISA
2
D: Possible translation initiation inhibitor
E: Possible translation initiation inhibitor
F: Possible translation initiation inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2557
Polymers44,8713
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-103 kcal/mol
Surface area14520 Å2
MethodPISA
3
G: Possible translation initiation inhibitor
H: Possible translation initiation inhibitor
I: Possible translation initiation inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1596
Polymers44,8713
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-90 kcal/mol
Surface area14720 Å2
MethodPISA
4
J: Possible translation initiation inhibitor
K: Possible translation initiation inhibitor
L: Possible translation initiation inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2557
Polymers44,8713
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-113 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.185, 142.239, 147.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Possible translation initiation inhibitor


Mass: 14956.951 Da / Num. of mol.: 12 / Fragment: sequence database residues 30-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA2473 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6N6Z0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Acetate pH 4.5, 30% PEG 8K. 0.2M Lithium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 62233 / % possible obs: 99.9 % / Redundancy: 12 % / Rmerge(I) obs: 0.119 / Χ2: 1.43 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.75-2.811.80.90530611.114100
2.8-2.8511.80.76230571.08399.8
2.85-2.911.80.65830781.09399.8
2.9-2.9611.90.55430881.11399.9
2.96-3.03120.48930591.129100
3.03-3.1120.3830531.1499.9
3.1-3.1712.10.29630881.18100
3.17-3.2612.10.2630781.21100
3.26-3.3612.20.20630821.291100
3.36-3.4612.30.17530891.35100
3.46-3.5912.30.14631051.36100
3.59-3.7312.30.12530931.503100
3.73-3.912.30.11231081.512100
3.9-4.1112.30.10131061.512100
4.11-4.3612.20.0931191.531100
4.36-4.712.10.0931251.67699.9
4.7-5.17120.08131501.507100
5.17-5.9211.80.09131481.725100
5.92-7.4611.50.08731992.233100
7.46-5011.40.07233472.29499.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.74→49.19 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.234 / WRfactor Rwork: 0.195 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.816 / SU B: 11.637 / SU ML: 0.235 / SU R Cruickshank DPI: 0.563 / SU Rfree: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3111 5 %RANDOM
Rwork0.204 ---
obs0.206 61952 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.25 Å2 / Biso mean: 56.456 Å2 / Biso min: 28.14 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å20 Å2
2--0.32 Å20 Å2
3---3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.74→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11606 0 70 25 11701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211900
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.96216184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3351530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01523.25480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.092151872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9751596
X-RAY DIFFRACTIONr_chiral_restr0.1060.21830
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219004
X-RAY DIFFRACTIONr_mcbond_it0.7061.57636
X-RAY DIFFRACTIONr_mcangle_it1.374212298
X-RAY DIFFRACTIONr_scbond_it2.03834264
X-RAY DIFFRACTIONr_scangle_it3.5674.53886
LS refinement shellResolution: 2.741→2.812 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 209 -
Rwork0.304 4012 -
all-4221 -
obs--92.87 %

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