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- PDB-2g40: Crystal structure of a duf162 family protein (dr_1909) from deino... -

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Basic information

Entry
Database: PDB / ID: 2g40
TitleCrystal structure of a duf162 family protein (dr_1909) from deinococcus radiodurans at 1.70 A resolution
Componentsconserved hypothetical protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyLUD domain / LUD domain / NagB/RpiA/CoA transferase-like / 5-formyltetrahydrofolate cyclo-ligase-like domain superfamily / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lactate utilization protein C
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (6459694) from Deinococcus radiodurans at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: 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 1.4May 29, 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: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)24,1091
Polymers24,1091
Non-polymers00
Water2,378132
1
A: conserved hypothetical protein

A: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)48,2172
Polymers48,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Unit cell
Length a, b, c (Å)53.410, 53.410, 118.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein conserved hypothetical protein


Mass: 24108.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: 6459694 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RT57
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.829.3
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop8.320.0% PEG-3350, 0.2M K3Citrate, No Buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop7.50.2M MgCl2, 30.0% PEG-400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 5.0.311
SYNCHROTRONSSRL BL1-520.918381, 0.979310, 0.978359
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDAug 26, 2004
ADSC QUANTUM 3152CCDJan 12, 20061m long Rh coated bent cylindrical mirror for horizontal and vertical focusing
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2Si(111) 2-crystal monochromator
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9183811
30.979311
40.9783591
ReflectionResolution: 1.7→27.28 Å / Num. obs: 19674 / % possible obs: 98.3 % / Biso Wilson estimate: 25.34 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.38
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.760.4982.813288337394.7
1.76-1.830.425418677356498.9
1.83-1.910.3665.320708336395.8
1.91-2.020.2797.125662377396.9
2.02-2.140.18510.721365340299
2.14-2.310.13313.723494364398.9
2.31-2.540.08221.825289358999.9
2.54-2.90.0726.225098353799.9
2.90.05737.234301363699.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→27.28 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.027 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.103
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ELECTRON DENSITIES FOR THE 37 N-TERMINAL RESIDUES AND FOR RESIDUES 188-198 ARE DISORDERED; THEREFORE, COORDINATES FOR ATOMS IN THESE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ELECTRON DENSITIES FOR THE 37 N-TERMINAL RESIDUES AND FOR RESIDUES 188-198 ARE DISORDERED; THEREFORE, COORDINATES FOR ATOMS IN THESE REGIONS ARE NOT INCLUDED IN THE MODEL. 3.THE DATA USED IN THE FINAL REFINEMENT WAS FROM A NATIVE CRYSTAL. THE REFINEMENT OF THE COORDINATES WAS RESTRAINED WITH THE EXPERIMENTAL PHASES FROM A CRYSTAL OF THE SELENOMETHIONINE-SUBSTITUTED PROTEIN THAT WAS USED FOR INITIAL PHASE DETERMINATION BY MULTIPLE WAVELENGTH ANOMALOUS DISPERSION.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 984 5 %RANDOM
Rwork0.178 ---
obs0.18 19611 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 0 132 1348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221254
X-RAY DIFFRACTIONr_bond_other_d0.0010.021210
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9661713
X-RAY DIFFRACTIONr_angle_other_deg0.7832782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.64622.65349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80515195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1851512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
X-RAY DIFFRACTIONr_nbd_refined0.2110.2252
X-RAY DIFFRACTIONr_nbd_other0.1850.21267
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2633
X-RAY DIFFRACTIONr_nbtor_other0.0810.2849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0790.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.210
X-RAY DIFFRACTIONr_mcbond_it1.7163876
X-RAY DIFFRACTIONr_mcbond_other0.4343338
X-RAY DIFFRACTIONr_mcangle_it2.31751325
X-RAY DIFFRACTIONr_scbond_it4.0898455
X-RAY DIFFRACTIONr_scangle_it5.93911387
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 77 -
Rwork0.259 1299 -
obs-1376 97.87 %
Refinement TLS params.Method: refined / Origin x: -21.6381 Å / Origin y: 13.7363 Å / Origin z: 1.7575 Å
111213212223313233
T-0.0668 Å2-0.0047 Å20.0176 Å2--0.0323 Å20.0241 Å2---0.0554 Å2
L1.4188 °2-0.0867 °20.6714 °2-1.0025 °2-0.082 °2--1.311 °2
S-0.0107 Å °-0.0629 Å °-0.0972 Å °-0.102 Å °-0.0071 Å °-0.0744 Å °0.0388 Å °0.0431 Å °0.0178 Å °
Refinement TLS groupSelection: ALL

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