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- PDB-1rki: Structure of pag5_736 from P. aerophilum with three disulphide bonds -

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Basic information

Entry
Database: PDB / ID: 1rki
TitleStructure of pag5_736 from P. aerophilum with three disulphide bonds
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / (beta-alpha-beta)x2 / beta-loop-beta-beta / CxxC motif
Function / homology
Function and homology information


PDO, CxxC motif / Protein of unknown function DUF3195 / : / Protein of unknown function (DUF3195) N-terminal domain / Protein of unknown function (DUF3195) C-terminal domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsBeeby, M. / Ryttersgaard, C. / Boutz, D.R. / Perry, L.J. / Yeates, T.O.
CitationJournal: Plos Biol. / Year: 2005
Title: The Genomics of Disulfide Bonding and Protein Stabilization in Thermophiles.
Authors: Beeby, M. / Ryttersgaard, C. / Boutz, D.R. / Perry, L.J. / Yeates, T.O.
History
DepositionNov 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 30, 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_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_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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5558
Polymers23,7922
Non-polymers7636
Water1,60389
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0883
Polymers11,8961
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4675
Polymers11,8961
Non-polymers5714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.483, 43.717, 52.717
Angle α, β, γ (deg.)90.00, 113.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein hypothetical protein


Mass: 11896.090 Da / Num. of mol.: 2 / Fragment: pag5_736
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q8ZYK2

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Non-polymers , 6 types, 95 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 8000, lithium sulphate, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONALS 8.2.221.1271
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJun 6, 2003
ADSC QUANTUM 3152CCDJul 12, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Osmic Confocal Max-FluxSINGLE WAVELENGTHMx-ray1
2Double crystal Si(1 1 1)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.12711
ReflectionResolution: 1.6→90 Å / Num. all: 28068 / Num. obs: 28068 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.125
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.495 / Num. unique all: 2174 / % possible all: 75

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 1.6→28.63 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.36 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.091 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23507 1409 5 %RANDOM
Rwork0.18409 ---
all0.18665 26648 --
obs0.18665 26648 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å2-1.46 Å2
2--2.69 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 47 89 1750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221706
X-RAY DIFFRACTIONr_bond_other_d0.0020.021580
X-RAY DIFFRACTIONr_angle_refined_deg2.272.0072289
X-RAY DIFFRACTIONr_angle_other_deg2.50833736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555196
X-RAY DIFFRACTIONr_chiral_restr0.1110.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021741
X-RAY DIFFRACTIONr_gen_planes_other0.010.02301
X-RAY DIFFRACTIONr_nbd_refined0.2070.2269
X-RAY DIFFRACTIONr_nbd_other0.240.21642
X-RAY DIFFRACTIONr_nbtor_other0.0940.2982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.25
X-RAY DIFFRACTIONr_mcbond_it1.3681.5993
X-RAY DIFFRACTIONr_mcangle_it2.41621641
X-RAY DIFFRACTIONr_scbond_it3.4943709
X-RAY DIFFRACTIONr_scangle_it5.5964.5640
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.419 65
Rwork0.378 1420
obs-1485
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)
11.9815-0.71120.6060.9589-0.08852.05890.0291-0.1462-0.0580.0465-0.05520.0024-0.0442-0.03820.02610.0606-0.02670.00870.0499-0.00290.0423-3.40525.816314.3336
22.45-0.2392.4730.90660.91594.96690.00720.20020.2309-0.1544-0.082-0.0095-0.27750.31110.07480.0933-0.0222-0.01530.0909-0.0170.02298.925511.642929.1303
30.82990.62530.16642.04890.89250.571-0.01990.0393-0.00090.0643-0.04410.1017-0.0733-0.04950.0640.04420.0130.00760.05590.00560.090718.273318.97264.9588
4-0.0485-0.0097-0.75761.33340.25452.60690.0052-0.0228-0.11880.1010.0497-0.01030.20480.0889-0.05490.06330.0032-0.00750.07150.02510.100513.6532-0.23264.8688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 70
2X-RAY DIFFRACTION2A71 - 101
3X-RAY DIFFRACTION3B1 - 70
4X-RAY DIFFRACTION4B71 - 97

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