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- PDB-3hhl: Crystal structure of methylated RPA0582 protein -

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Basic information

Entry
Database: PDB / ID: 3hhl
TitleCrystal structure of methylated RPA0582 protein
Components(RPA0582) x 4
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALPHA-BETA-BARREL / PSI-2 / PROTEIN STRUCTURE INITIATIVE / REDUCTIVE METHYLATION / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Domain 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
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DUF1330 domain-containing protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSledz, P. / Niedzialkowska, E. / Chruszcz, M. / Porebski, P. / Yim, V. / Kudritska, M. / Zimmerman, M.D. / Evdokimova, E. / Savchenko, A. / Edwards, A. ...Sledz, P. / Niedzialkowska, E. / Chruszcz, M. / Porebski, P. / Yim, V. / Kudritska, M. / Zimmerman, M.D. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of methylated RPA0582 protein
Authors: Sledz, P. / Niedzialkowska, E. / Chruszcz, M. / Porebski, P. / Yim, V. / Kudritska, M. / Zimmerman, M.D. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W.
History
DepositionMay 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.3Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,49732
Polymers65,3094
Non-polymers4,18828
Water4,522251
1
A: RPA0582
D: RPA0582
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,59415
Polymers32,6552
Non-polymers1,93913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-59 kcal/mol
Surface area13640 Å2
MethodPISA
2
B: RPA0582
C: RPA0582
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,90317
Polymers32,6542
Non-polymers2,24915
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-61 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.012, 193.012, 117.965
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
11C-143-

SO4

21C-201-

HOH

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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: MLY / End label comp-ID: MLY / Refine code: 6 / Auth seq-ID: 1 - 135 / Label seq-ID: 2 - 136

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

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein RPA0582


Mass: 16333.947 Da / Num. of mol.: 1 / Mutation: F61S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA0582 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90
#2: Protein RPA0582


Mass: 16306.900 Da / Num. of mol.: 1 / Mutation: F61S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA0582 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90
#3: Protein RPA0582


Mass: 16346.965 Da / Num. of mol.: 1 / Mutation: F61S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA0582 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90
#4: Protein RPA0582


Mass: 16320.928 Da / Num. of mol.: 1 / Mutation: F61S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: CGA009 / Gene: RPA0582 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RP / References: UniProt: Q6NC90

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Non-polymers , 10 types, 279 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O9
#12: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#13: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE MUTATION F61S IS A CLONING ARTIFACT THAT WAS CONFIRMED BY SEQUENCING.

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M AMMONIUM SULPHATE, 25% PEG3350, 0.1M HEPES pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9787 / Wavelength: 0.9787 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 31, 2007 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.65→96.67 Å / Num. all: 47581 / Num. obs: 47581 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 73.8 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 24.26
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2405 / Rsym value: 0.596 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.5.0089refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DCA

3dca


Resolution: 2.65→32.17 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.676 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.213 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2400 5.1 %RANDOM
Rwork0.178 ---
all0.18 47443 --
obs0.18 47443 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.12 Å20 Å2
2---0.25 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.65→32.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4299 0 270 251 4820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214789
X-RAY DIFFRACTIONr_bond_other_d0.0060.023471
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9936405
X-RAY DIFFRACTIONr_angle_other_deg0.83738314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6285562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74321.931233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04715744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5441560
X-RAY DIFFRACTIONr_chiral_restr0.0820.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215159
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021017
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_it0.91.52755
X-RAY DIFFRACTIONr_mcbond_other0.1351.51090
X-RAY DIFFRACTIONr_mcangle_it1.7124436
X-RAY DIFFRACTIONr_scbond_it2.44632034
X-RAY DIFFRACTIONr_scangle_it4.1044.51964
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: 1745 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Cloose positional0.345
Aloose positional0.345
Bloose positional0.355
Dloose positional0.365
Cloose thermal1.2910
Aloose thermal0.9810
Bloose thermal0.8710
Dloose thermal1.1210
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 200 -
Rwork0.31 3320 -
obs--99.35 %
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)
11.0429-0.25720.55590.9033-0.08062.8592-0.05560.1485-0.066-0.14250.0887-0.04750.25020.3484-0.0330.0879-0.00620.04580.13-0.05220.0599-18.42760.02315.066
22.0030.90570.48922.05160.73141.2776-0.02280.2247-0.2193-0.02850.0573-0.3507-0.06190.1964-0.03460.00880.00660.01250.09760.02930.14542.17278.38439.421
31.11930.06180.03953.2175-0.14271.0680.0409-0.1159-0.13220.3811-0.01630.0772-0.0655-0.0603-0.02450.0982-0.0269-0.01210.10360.05490.0378-5.60191.0557.582
42.62770.54090.77691.11220.29981.2449-0.1429-0.00620.3361-0.08520.06650.1148-0.23630.13150.07640.1272-0.05790.00330.03530.0020.0834-33.43777.4579.24
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 135
2X-RAY DIFFRACTION2B1 - 135
3X-RAY DIFFRACTION3C1 - 135
4X-RAY DIFFRACTION4D1 - 135

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