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- PDB-2p1i: Plasmodium yoelii Ribonucleotide Reductase Subunit R2 (PY03671) -

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Basic information

Entry
Database: PDB / ID: 2p1i
TitlePlasmodium yoelii Ribonucleotide Reductase Subunit R2 (PY03671)
ComponentsRibonucleotide reductase, small chain
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / F222 twinning / plasmodb PY03671 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ribonucleotide reductase, small chain
Similarity search - Component
Biological speciesPlasmodium yoelii yoelii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWernimont, A.K. / Dong, A. / Choe, J. / Gao, M. / Walker, J. / Lew, J. / Alam, Z. / Zhao, Y. / Nordlund, P. / Arrowsmith, C.H. ...Wernimont, A.K. / Dong, A. / Choe, J. / Gao, M. / Walker, J. / Lew, J. / Alam, Z. / Zhao, Y. / Nordlund, P. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Plasmodium yoelii Ribonucleotide Reductase Subunit R2 (PY03671)
Authors: Wernimont, A.K. / Dong, A. / Choe, J. / Gao, M. / Walker, J. / Lew, J. / Alam, Z. / Zhao, Y. / Nordlund, P. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Artz, J.D.
History
DepositionMar 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonucleotide reductase, small chain
B: Ribonucleotide reductase, small chain
C: Ribonucleotide reductase, small chain
D: Ribonucleotide reductase, small chain
E: Ribonucleotide reductase, small chain
F: Ribonucleotide reductase, small chain
G: Ribonucleotide reductase, small chain
H: Ribonucleotide reductase, small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,38416
Polymers323,9378
Non-polymers4478
Water2,180121
1
A: Ribonucleotide reductase, small chain
D: Ribonucleotide reductase, small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0964
Polymers80,9842
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonucleotide reductase, small chain
C: Ribonucleotide reductase, small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0964
Polymers80,9842
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ribonucleotide reductase, small chain
F: Ribonucleotide reductase, small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0964
Polymers80,9842
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Ribonucleotide reductase, small chain
H: Ribonucleotide reductase, small chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0964
Polymers80,9842
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)192.040, 153.460, 143.360
Angle α, β, γ (deg.)90.00, 132.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H
171A
181B
191C
201D
211E
221F
231G
241H
251A
261B
271C
281D
291E
301F
311G
321H
331A
341B
351C
361D
371E
381F
391G
401H

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRLEULEU3AA48 - 8048 - 80
21TYRTYRLEULEU3BB48 - 8048 - 80
31TYRTYRLEULEU3CC48 - 8048 - 80
41TYRTYRLEULEU3DD48 - 8048 - 80
51TYRTYRLEULEU3EE48 - 8048 - 80
61TYRTYRLEULEU3FF48 - 8048 - 80
71TYRTYRLEULEU3GG48 - 8048 - 80
81TYRTYRLEULEU3HH48 - 8048 - 80
92HISHISGLUGLU3AA86 - 14886 - 148
102HISHISGLUGLU3BB86 - 14886 - 148
112HISHISGLUGLU3CC86 - 14886 - 148
122HISHISGLUGLU3DD86 - 14886 - 148
132HISHISGLUGLU3EE86 - 14886 - 148
142HISHISGLUGLU3FF86 - 14886 - 148
152HISHISGLUGLU3GG86 - 14886 - 148
162HISHISGLUGLU3HH86 - 14886 - 148
173PROPROLEULEU3AA162 - 239162 - 239
183PROPROLEULEU3BB162 - 239162 - 239
193PROPROLEULEU3CC162 - 239162 - 239
203PROPROLEULEU3DD162 - 239162 - 239
213PROPROLEULEU3EE162 - 239162 - 239
223PROPROLEULEU3FF162 - 239162 - 239
233PROPROLEULEU3GG162 - 239162 - 239
243PROPROLEULEU3HH162 - 239162 - 239
254ASNASNASPASP3AA242 - 271242 - 271
264ASNASNASPASP3BB242 - 271242 - 271
274ASNASNASPASP3CC242 - 271242 - 271
284ASNASNASPASP3DD242 - 271242 - 271
294ASNASNASPASP3EE242 - 271242 - 271
304ASNASNASPASP3FF242 - 271242 - 271
314ASNASNASPASP3GG242 - 271242 - 271
324ASNASNASPASP3HH242 - 271242 - 271
335ILEILETRPTRP2AA273 - 309273 - 309
345ILEILETRPTRP2BB273 - 309273 - 309
355ILEILETRPTRP2CC273 - 309273 - 309
365ILEILETRPTRP2DD273 - 309273 - 309
375ILEILETRPTRP2EE273 - 309273 - 309
385ILEILETRPTRP2FF273 - 309273 - 309
395ILEILETRPTRP2GG273 - 309273 - 309
405ILEILETRPTRP2HH273 - 309273 - 309

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Components

#1: Protein
Ribonucleotide reductase, small chain


Mass: 40492.129 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii yoelii (eukaryote) / Species: Plasmodium yoelii / Strain: 17XNL / Gene: PY03671 / Plasmid: p15-TEV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q7RIF3
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.0 M Sodium formate, 100 mM Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97972 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 104627 / Num. obs: 104627 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Rsym value: 0.048 / Net I/σ(I): 14.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.767 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PIY

1piy


Resolution: 2.7→19.99 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.81 / SU B: 44.405 / SU ML: 0.484 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.993 / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA IS TWINNED, C2 PSEUDO F222. AUTHORS STATE THAT THIS PARTICULAR TWINNING WAS UNUSUAL AND VERY DIFFICULT TO DIAGNOSE
RfactorNum. reflection% reflectionSelection details
Rfree0.36797 3552 4.8 %RANDOM
Rwork0.3038 ---
obs0.30692 70611 100 %-
all-70611 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.29 Å2
2---0.38 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16775 0 8 121 16904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02217209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.93523205
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.68952029
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.94924.954868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.316153058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0771555
X-RAY DIFFRACTIONr_chiral_restr0.1410.22519
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212959
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2920.210142
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.211695
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2686
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5080.2511
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4510.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6341.510555
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.164216467
X-RAY DIFFRACTIONr_scbond_it2.15137741
X-RAY DIFFRACTIONr_scangle_it3.1034.56738
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A940tight positional0.090.05
2B940tight positional0.080.05
3C940tight positional0.070.05
4D940tight positional0.090.05
5E940tight positional0.080.05
6F940tight positional0.080.05
7G940tight positional0.080.05
8H940tight positional0.070.05
1A155medium positional0.60.5
2B155medium positional0.710.5
3C155medium positional0.650.5
4D155medium positional0.570.5
5E155medium positional0.760.5
6F155medium positional0.630.5
7G155medium positional0.660.5
8H155medium positional0.750.5
1A824loose positional0.75
2B824loose positional0.815
3C824loose positional0.845
4D824loose positional0.695
5E824loose positional0.695
6F824loose positional0.785
7G824loose positional0.775
8H824loose positional0.755
1A940tight thermal0.220.5
2B940tight thermal0.170.5
3C940tight thermal0.160.5
4D940tight thermal0.240.5
5E940tight thermal0.170.5
6F940tight thermal0.160.5
7G940tight thermal0.150.5
8H940tight thermal0.140.5
1A155medium thermal1.492
2B155medium thermal1.242
3C155medium thermal1.052
4D155medium thermal1.552
5E155medium thermal1.382
6F155medium thermal1.32
7G155medium thermal1.122
8H155medium thermal1.12
1A824loose thermal3.2110
2B824loose thermal3.1510
3C824loose thermal2.9910
4D824loose thermal3.3710
5E824loose thermal3.1610
6F824loose thermal2.6810
7G824loose thermal2.7910
8H824loose thermal2.6610
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 226 -
Rwork0.319 4689 -
obs--100 %

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