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- PDB-3fov: Crystal structure of protein RPA0323 of unknown function from Rho... -

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Basic information

Entry
Database: PDB / ID: 3fov
TitleCrystal structure of protein RPA0323 of unknown function from Rhodopseudomonas palustris
ComponentsUPF0102 protein RPA0323
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC7380 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


nucleic acid binding
Similarity search - Function
Uncharacterised protein family UPF0102 / Uncharacterised protein family UPF0102 / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / UPF0102 protein RPA0323
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsOsipiuk, J. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of protein RPA0323 of unknown function from Rhodopseudomonas palustris.
Authors: Osipiuk, J. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionJan 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0102 protein RPA0323
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8383
Polymers14,7141
Non-polymers1242
Water1,58588
1
A: UPF0102 protein RPA0323
hetero molecules

A: UPF0102 protein RPA0323
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6776
Polymers29,4292
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area970 Å2
ΔGint-7.4 kcal/mol
Surface area11250 Å2
MethodPISA
2
A: UPF0102 protein RPA0323
hetero molecules

A: UPF0102 protein RPA0323
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6776
Polymers29,4292
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1280 Å2
ΔGint-15.4 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.341, 44.747, 32.661
Angle α, β, γ (deg.)90.000, 108.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-184-

HOH

DetailsAUTHORS STATE THAT THE ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein UPF0102 protein RPA0323


Mass: 14714.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA0323 / Plasmid: pET15b modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6NCZ4
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20% PEG 3350, 0.2 M Magnesium nitrate, 0.3 M NSDB-256, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.88→26.3 Å / Num. all: 8519 / Num. obs: 8519 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.211 / Net I/σ(I): 40.099
Reflection shellResolution: 1.88→1.94 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 6.2 / Num. unique all: 492 / Χ2: 1.492 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→26.27 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 8.988 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.222 407 4.8 %RANDOM
Rwork0.188 ---
all0.19 8456 --
obs0.19 8456 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.54 Å2 / Biso mean: 23.636 Å2 / Biso min: 12.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.28 Å2
2--0.4 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.88→26.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 8 88 894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022849
X-RAY DIFFRACTIONr_bond_other_d0.0010.02592
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9551156
X-RAY DIFFRACTIONr_angle_other_deg0.91431424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5185109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32721.8643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17615136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5981512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02190
X-RAY DIFFRACTIONr_mcbond_it0.9221.5532
X-RAY DIFFRACTIONr_mcbond_other0.2161.5205
X-RAY DIFFRACTIONr_mcangle_it1.7062843
X-RAY DIFFRACTIONr_scbond_it2.6143317
X-RAY DIFFRACTIONr_scangle_it4.3734.5308
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 29 -
Rwork0.296 548 -
all-577 -
obs-677 91.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.11581.99791.50984.17160.89042.63570.0578-0.0378-0.22430.05430.0297-0.3080.01080.1364-0.08740.02640.0094-0.03690.0331-0.010.066117.278314.471716.7631
27.5267-2.18271.67773.2113-1.45890.74080.0243-0.0049-0.3347-0.00550.03710.02630.0052-0.0185-0.06140.0359-0.0165-0.00060.02080.00450.05625.94465.3644.9739
36.81710.075-0.17494.74031.50933.5986-0.08380.25340.189-0.09160.1556-0.1807-0.3472-0.0735-0.07170.05950.0039-0.01570.01980.00490.029711.208817.982912.5569
44.40716.4330.96499.94121.43460.2131-0.11560.09280.24560.06420.09030.0821-0.02160.02130.02540.2203-0.0144-0.02150.15360.00880.22369.75622.7656-0.6856
51.9104-1.06490.37470.6997-1.03356.5364-0.04630.1457-0.19020.058-0.070.0794-0.2848-0.12630.11630.043-0.0065-0.00540.03470.00390.06973.284911.76174.8241
62.9171.6230.17223.1996-0.40932.4389-0.0227-0.25430.15470.08510.06810.0925-0.20810.0604-0.04540.04450.0143-0.00670.0548-0.01960.01657.494516.446413.6814
79.54830.6034-1.32462.20090.14554.5211-0.30980.06230.461-0.00460.21870.3133-0.2163-0.34060.09120.09810.0079-0.01690.05320.02030.06349.542124.15119.2383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 43
2X-RAY DIFFRACTION2A44 - 51
3X-RAY DIFFRACTION3A52 - 69
4X-RAY DIFFRACTION4A76 - 81
5X-RAY DIFFRACTION5A82 - 95
6X-RAY DIFFRACTION6A96 - 117
7X-RAY DIFFRACTION7A118 - 130

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