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- PDB-3dca: Crystal structure of the RPA0582- protein of unknown function fro... -

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Basic information

Entry
Database: PDB / ID: 3dca
TitleCrystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target
ComponentsRPA0582
Keywordsstructural genomics / unknown function / Alpha-beta-barrel / SAD / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyDomain of unknown function DUF1330 / Domain of unknown function (DUF1330) / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / DUF1330 domain-containing protein
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.35 Å
AuthorsSledz, P. / Wang, S. / Chruszcz, M. / Yim, V. / Kudritska, M. / Evdokimova, E. / Turk, D. / Savchenko, A. / Edwards, A. / Joachimiak, A. ...Sledz, P. / Wang, S. / Chruszcz, M. / Yim, V. / Kudritska, M. / Evdokimova, E. / Turk, D. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target
Authors: Sledz, P. / Wang, S. / Chruszcz, M. / Yim, V. / Kudritska, M. / Evdokimova, E. / Turk, D. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionJun 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RPA0582
B: RPA0582
C: RPA0582
D: RPA0582
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,65610
Polymers65,0804
Non-polymers5766
Water00
1
A: RPA0582
B: RPA0582
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8285
Polymers32,5402
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-31 kcal/mol
Surface area12660 Å2
MethodPISA
2
C: RPA0582
D: RPA0582
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8285
Polymers32,5402
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-29 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.495, 193.495, 118.848
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-143-

SO4

21A-143-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 1 / Auth seq-ID: 2 - 133 / Label seq-ID: 2 - 133

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
RPA0582


Mass: 16269.880 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA0582 / Plasmid: P15TV LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
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: 6.58 Å3/Da / Density % sol: 81.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M AMMONIUM SULPHATE, 0.1M NA CACODILATE PH6.5, 30%PEG8K, , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2007 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.9791
ReflectionResolution: 3.35→36.59 Å / Num. all: 22256 / Num. obs: 22256 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 98.16 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 13.716
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 2 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2257 / Rsym value: 0.426 / % possible all: 93.2

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Processing

Software
NameVersionClassification
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
MAINmodel building
REFMAC5.5.0017refinement
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
DMphasing
MAINphasing
MAINrefinement
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.35→36.59 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.876 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.615 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1133 5.1 %RANDOM
Rwork0.273 ---
all0.274 22147 --
obs0.274 22147 92.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 3.35→36.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 30 0 3894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213996
X-RAY DIFFRACTIONr_bond_other_d00.022607
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9515466
X-RAY DIFFRACTIONr_angle_other_deg4.2536277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40621.687166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87115512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5791536
X-RAY DIFFRACTIONr_chiral_restr0.0730.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214551
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02872
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1525 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Auth asym-IDRms dev position (Å)
A0.05
B0.07
C0.05
D0.06
LS refinement shellResolution: 3.35→3.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 76 -
Rwork0.325 1558 -
obs-2257 93.21 %

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