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- PDB-4idi: Crystal Structure of Rurm1-related protein from Plasmodium Yoelii... -

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Basic information

Entry
Database: PDB / ID: 4idi
TitleCrystal Structure of Rurm1-related protein from Plasmodium Yoelii, PY06420
ComponentsOryza sativa Rurm1-related
KeywordsPROTEIN BINDING / Structural Genomics / Structural Genomics Consortium / SGC / beta grasp
Function / homology
Function and homology information


tRNA thio-modification / protein urmylation / tRNA wobble uridine modification / cytosol
Similarity search - Function
Ubiquitin-related modifier 1 / Urm1 (Ubiquitin related modifier) / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-related modifier 1 homolog
Similarity search - Component
Biological speciesPlasmodium yoelii yoelii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsWernimont, A.K. / Tempel, W. / Lew, J. / Walker, J. / Arrowsmith, C.H. / Edwards, A.M. / Schapira, M. / Bountra, C. / Hui, R. / Artz, J.D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Rurm1-related protein from Plasmodium Yoelii, PY06420
Authors: Wernimont, A.K. / Tempel, W. / Lew, J. / Walker, J. / Arrowsmith, C.H. / Edwards, A.M. / Schapira, M. / Bountra, C. / Hui, R. / Artz, J.D.
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Oryza sativa Rurm1-related
B: Oryza sativa Rurm1-related
C: Oryza sativa Rurm1-related
D: Oryza sativa Rurm1-related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1155
Polymers67,0234
Non-polymers921
Water4,288238
1
A: Oryza sativa Rurm1-related


Theoretical massNumber of molelcules
Total (without water)16,7561
Polymers16,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Oryza sativa Rurm1-related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8482
Polymers16,7561
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Oryza sativa Rurm1-related


Theoretical massNumber of molelcules
Total (without water)16,7561
Polymers16,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Oryza sativa Rurm1-related


Theoretical massNumber of molelcules
Total (without water)16,7561
Polymers16,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.590, 72.720, 107.510
Angle α, β, γ (deg.)90.00, 92.64, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein
Oryza sativa Rurm1-related


Mass: 16755.656 Da / Num. of mol.: 4 / Mutation: L70(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii yoelii (eukaryote) / Gene: PY06420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7RAS9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 1.9 Å3/Da / Density % sol: 35.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 25 % PEG 3350, 0.2 M NaCl, 0.1 M Na Cacodylate, 0.1 ug/ml chymotrypsin, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97942 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 39505 / Num. obs: 39268 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 25.56 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-1.975.10.512.14195.3
1.97-2.055.80.4373.08198.8
2.05-2.146.40.358199.9
2.14-2.256.80.2931100
2.25-2.3970.2591100
2.39-2.5870.2191100
2.58-2.8470.1781100
2.84-3.257.10.1431100
3.25-4.097.40.1151100
4.09-507.50.0981100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
BALBESphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.2 Å / Cor.coef. Fo:Fc: 0.9348 / Cor.coef. Fo:Fc free: 0.9205 / Occupancy max: 1 / Occupancy min: 0.3 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 1971 5.04 %RANDOM
Rwork0.2271 ---
obs0.2284 39123 98.79 %-
all-39602 --
Displacement parametersBiso mean: 30.33 Å2
Baniso -1Baniso -2Baniso -3
1-3.7563 Å20 Å20.2638 Å2
2--0.7844 Å20 Å2
3----4.5406 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 6 238 4090
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014028HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075436HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1491SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes123HARMONIC2
X-RAY DIFFRACTIONt_gen_planes561HARMONIC5
X-RAY DIFFRACTIONt_it4028HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion18.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion536SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4654SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2486 145 5.71 %
Rwork0.2175 2396 -
all0.2193 2541 -
obs--98.79 %
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)
12.8882-0.6126-0.1282.6376-0.6261.5878-0.0464-0.0777-0.1931-0.1177-0.02890.00740.21550.04350.0752-0.1226-0.00560.0122-0.07830.01850.021822.897551.908194.3765
23.884-0.67340.05292.99360.71111.4797-0.0624-0.05590.2765-0.12180.0151-0.0418-0.2081-0.05380.0472-0.141-0.0042-0.0038-0.087-0.01530.031616.129481.608194.4276
32.93250.7981-0.18243.1296-1.09971.7042-0.00940.04250.25350.1248-0.05250.0558-0.24380.07270.0619-0.0382-0.0034-0.0025-0.10030.0091-0.056925.548862.872766.694
43.15720.6172-0.04552.77310.70431.4841-0.04120.0423-0.27940.1011-0.01050.01750.1645-0.06330.0516-0.050.00280.0119-0.0905-0.0093-0.039818.191333.658266.642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 122
2X-RAY DIFFRACTION2{ B|* }B1 - 122
3X-RAY DIFFRACTION3{ C|* }C1 - 122
4X-RAY DIFFRACTION4{ D|* }D2 - 122

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