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- PDB-2j4j: Crystal structure of uridylate kinase from Sulfolobus solfataricu... -

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Basic information

Entry
Database: PDB / ID: 2j4j
TitleCrystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UMP and AMPPCP to 2.1 Angstrom resolution
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE / NUCLEOSIDE MONOPHOSPHATE KINASE / KINASE / UMP KINASE / ASPARTOKINASE FOLD / PYRIMIDINE NUCLEOTIDE SYNTHESIS / PYRIMIDINE BIOSYNTHESIS
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Uridylate kinase, archaeal/spirochete, putative / Uridylate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4TC / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / URIDINE-5'-MONOPHOSPHATE / Uridylate kinase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJensen, K.S. / Johansson, E. / Jensen, K.F.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and Enzymatic Investigation of the Sulfolobus Solfataricus Uridylate Kinase Shows Competitive Utp Inhibition and the Lack of GTP Stimulation
Authors: Jensen, K.S. / Johansson, E. / Jensen, K.F.
History
DepositionSep 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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.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 / _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: URIDYLATE KINASE
B: URIDYLATE KINASE
C: URIDYLATE KINASE
D: URIDYLATE KINASE
E: URIDYLATE KINASE
F: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,46225
Polymers150,1016
Non-polymers5,36119
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.174, 126.438, 134.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNILEILE1AA2 - 42 - 4
211ASNASNILEILE1BB2 - 42 - 4
311ASNASNILEILE1CC2 - 42 - 4
411ASNASNILEILE1DD2 - 42 - 4
511ASNASNILEILE1EE2 - 42 - 4
611ASNASNILEILE1FF2 - 42 - 4
121LYSLYSGLUGLU1AA6 - 146 - 14
221LYSLYSGLUGLU1BB6 - 146 - 14
321LYSLYSGLUGLU1CC6 - 146 - 14
421LYSLYSGLUGLU1DD6 - 146 - 14
521LYSLYSGLUGLU1EE6 - 146 - 14
621LYSLYSGLUGLU1FF6 - 146 - 14
131LEULEUARGARG1AA23 - 2423 - 24
231LEULEUARGARG1BB23 - 2423 - 24
331LEULEUARGARG1CC23 - 2423 - 24
431LEULEUARGARG1DD23 - 2423 - 24
531LEULEUARGARG1EE23 - 2423 - 24
631LEULEUARGARG1FF23 - 2423 - 24
141LEULEUALAALA1AA30 - 4730 - 47
241LEULEUALAALA1BB30 - 4730 - 47
341LEULEUALAALA1CC30 - 4730 - 47
441LEULEUALAALA1DD30 - 4730 - 47
541LEULEUALAALA1EE30 - 4730 - 47
641LEULEUALAALA1FF30 - 4730 - 47
151TYRTYRLEULEU1AA50 - 8350 - 83
251TYRTYRLEULEU1BB50 - 8350 - 83
351TYRTYRLEULEU1CC50 - 8350 - 83
451TYRTYRLEULEU1DD50 - 8350 - 83
551TYRTYRLEULEU1EE50 - 8350 - 83
651TYRTYRLEULEU1FF50 - 8350 - 83
161ASPASPVALVAL1AA85 - 10985 - 109
261ASPASPVALVAL1BB85 - 10985 - 109
361ASPASPVALVAL1CC85 - 10985 - 109
461ASPASPVALVAL1DD85 - 10985 - 109
561ASPASPVALVAL1EE85 - 10985 - 109
661ASPASPVALVAL1FF85 - 10985 - 109
171GLYGLYSERSER1AA111 - 132111 - 132
271GLYGLYSERSER1BB111 - 132111 - 132
371GLYGLYSERSER1CC111 - 132111 - 132
471GLYGLYSERSER1DD111 - 132111 - 132
571GLYGLYSERSER1EE111 - 132111 - 132
671GLYGLYSERSER1FF111 - 132111 - 132
181THRTHRASNASN1AA134 - 140134 - 140
281THRTHRASNASN1BB134 - 140134 - 140
381THRTHRASNASN1CC134 - 140134 - 140
481THRTHRASNASN1DD134 - 140134 - 140
581THRTHRASNASN1EE134 - 140134 - 140
681THRTHRASNASN1FF134 - 140134 - 140
191ASPASPVALVAL1AA142 - 144142 - 144
291ASPASPVALVAL1BB142 - 144142 - 144
391ASPASPVALVAL1CC142 - 144142 - 144
491ASPASPVALVAL1DD142 - 144142 - 144
591ASPASPVALVAL1EE142 - 144142 - 144
691ASPASPVALVAL1FF142 - 144142 - 144
1101TYRTYRTYRTYR6AA145145
2101TYRTYRTYRTYR6BB145145
3101TYRTYRTYRTYR6CC145145
4101TYRTYRTYRTYR6DD145145
5101TYRTYRTYRTYR6EE145145
6101TYRTYRTYRTYR6FF145145
1111ASPASPPROPRO6AA148 - 149148 - 149
2111ASPASPPROPRO6BB148 - 149148 - 149
3111ASPASPPROPRO6CC148 - 149148 - 149
4111ASPASPPROPRO6DD148 - 149148 - 149
5111ASPASPPROPRO6EE148 - 149148 - 149
6111ASPASPPROPRO6FF148 - 149148 - 149
1121LEULEUPROPRO1AA157 - 159157 - 159
2121LEULEUPROPRO1BB157 - 159157 - 159
3121LEULEUPROPRO1CC157 - 159157 - 159
4121LEULEUPROPRO1DD157 - 159157 - 159
5121LEULEUPROPRO1EE157 - 159157 - 159
6121LEULEUPROPRO1FF157 - 159157 - 159
1131LEULEUTHRTHR1AA161 - 163161 - 163
2131LEULEUTHRTHR1BB161 - 163161 - 163
3131LEULEUTHRTHR1CC161 - 163161 - 163
4131LEULEUTHRTHR1DD161 - 163161 - 163
5131LEULEUTHRTHR1EE161 - 163161 - 163
6131LEULEUTHRTHR1FF161 - 163161 - 163
1141ASPASPLEULEU1AA165 - 166165 - 166
2141ASPASPLEULEU1BB165 - 166165 - 166
3141ASPASPLEULEU1CC165 - 166165 - 166
4141ASPASPLEULEU1DD165 - 166165 - 166
5141ASPASPLEULEU1EE165 - 166165 - 166
6141ASPASPLEULEU1FF165 - 166165 - 166
1151LYSLYSLEULEU1AA168 - 170168 - 170
2151LYSLYSLEULEU1BB168 - 170168 - 170
3151LYSLYSLEULEU1CC168 - 170168 - 170
4151LYSLYSLEULEU1DD168 - 170168 - 170
5151LYSLYSLEULEU1EE168 - 170168 - 170
6151LYSLYSLEULEU1FF168 - 170168 - 170
1161LEULEUSERSER1AA183 - 195183 - 195
2161LEULEUSERSER1BB183 - 195183 - 195
3161LEULEUSERSER1CC183 - 195183 - 195
4161LEULEUSERSER1DD183 - 195183 - 195
5161LEULEUSERSER1EE183 - 195183 - 195
6161LEULEUSERSER1FF183 - 195183 - 195
1171ILEILEILEILE1AA197197
2171ILEILEILEILE1BB197197
3171ILEILEILEILE1CC197197
4171ILEILEILEILE1DD197197
5171ILEILEILEILE1EE197197
6171ILEILEILEILE1FF197197
1181VALVALTYRTYR1AA199 - 204199 - 204
2181VALVALTYRTYR1BB199 - 204199 - 204
3181VALVALTYRTYR1CC199 - 204199 - 204
4181VALVALTYRTYR1DD199 - 204199 - 204
5181VALVALTYRTYR1EE199 - 204199 - 204
6181VALVALTYRTYR1FF199 - 204199 - 204
1191LYSLYSLEULEU1AA206 - 207206 - 207
2191LYSLYSLEULEU1BB206 - 207206 - 207
3191LYSLYSLEULEU1CC206 - 207206 - 207
4191LYSLYSLEULEU1DD206 - 207206 - 207
5191LYSLYSLEULEU1EE206 - 207206 - 207
6191LYSLYSLEULEU1FF206 - 207206 - 207
1201ILEILELEULEU1AA211 - 214211 - 214
2201ILEILELEULEU1BB211 - 214211 - 214
3201ILEILELEULEU1CC211 - 214211 - 214
4201ILEILELEULEU1DD211 - 214211 - 214
5201ILEILELEULEU1EE211 - 214211 - 214
6201ILEILELEULEU1FF211 - 214211 - 214
1211GLYGLYGLYGLY1AA216216
2211GLYGLYGLYGLY1BB216216
3211GLYGLYGLYGLY1CC216216
4211GLYGLYGLYGLY1DD216216
5211GLYGLYGLYGLY1EE216216
6211GLYGLYGLYGLY1FF216216
1221VALVALVALVAL1AA219 - 226219 - 226
2221VALVALVALVAL1BB219 - 226219 - 226
3221VALVALVALVAL1CC219 - 226219 - 226
4221VALVALVALVAL1DD219 - 226219 - 226
5221VALVALVALVAL1EE219 - 226219 - 226
6221VALVALVALVAL1FF219 - 226219 - 226
112COCOCOCO1AJ230
212COCOCOCO1BN230

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.99999, -0.00216, 0.00324), (-0.00255, 0.99191, -0.12689), (-0.00294, -0.12689, -0.99191)141.51093, 9.03749, 138.7265
2given(0.69157, -0.42493, -0.58409), (0.36619, -0.49076, 0.79061), (-0.6226, -0.76065, -0.18379)85.68054, 11.24317, 167.07106
3given(-0.68432, -0.35994, 0.63415), (-0.34925, -0.60164, -0.71837), (0.6401, -0.71308, 0.286)98.96736, 167.51237, 44.29635
4given(0.68937, 0.36264, -0.6271), (-0.43301, -0.48771, -0.75805), (-0.58075, 0.79412, -0.17919)41.59177, 169.32841, 71.28992
5given(-0.68758, 0.44065, 0.57711), (0.44059, -0.37857, 0.81398), (0.57716, 0.81395, 0.06614)55.18678, -2.07822, -28.14243

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
URIDYLATE KINASE / UK / URIDINE MONOPHOSPHATE KINASE / UMP KINASE


Mass: 25016.873 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97ZE2, UMP kinase

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Non-polymers , 6 types, 356 molecules

#2: Chemical
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-4TC / P1-(5'-ADENOSINE)P4-(5'-URIDINE)-BETA,GAMMA-METHYLENE TETRAPHOSPHATE


Mass: 811.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N7O20P4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CRYSTALLIZED ENZYME WAS PREPARED WITH ONLY ONE MET RESIDUE IN THE N-TERMINAL, IN CONTRAST TO ...THE CRYSTALLIZED ENZYME WAS PREPARED WITH ONLY ONE MET RESIDUE IN THE N-TERMINAL, IN CONTRAST TO THE DATABASE SEQUENCE.

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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: 2.44 Å3/Da / Density % sol: 46.7 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK AND 2MM UMP. 2MM AMPPCP AND 5 MM MGCL2 MIXED WITH 2 UL MOTHER SOLUTION. MOTHER SOLUTION: 0.8 M 1,6-HEXANEDIOL, 5 MM ...Details: PROTEIN SOLUTION (2UL) IN 10 MM TRIS/CL PH 7.6 WITH 4.6 MG/ML SSUMPK AND 2MM UMP. 2MM AMPPCP AND 5 MM MGCL2 MIXED WITH 2 UL MOTHER SOLUTION. MOTHER SOLUTION: 0.8 M 1,6-HEXANEDIOL, 5 MM COCL2, AND 0.1 M SODIUM ACETATE, PH 4.6. HANGING DROP VAPOR DIFFUSION TECHNIQUE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.085
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2004 / Details: VERTICALLY FOCUSING CYLINDRICAL MIRROR
RadiationMonochromator: SINGLE ASYMMETRICALLY CUT SI(111) CRYSTAL WITH HORIZONTAL DIFFRACTION PLANE
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.085 Å / Relative weight: 1
ReflectionResolution: 2.1→91.29 Å / Num. obs: 86630 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BMU - WITHOUT LIGANDS

2bmu


Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.208 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4353 5 %RANDOM
Rwork0.215 ---
obs0.216 82168 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10212 0 319 337 10868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210688
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210126
X-RAY DIFFRACTIONr_angle_refined_deg1.5592.01614523
X-RAY DIFFRACTIONr_angle_other_deg0.889323467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96351294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74724.171434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.049151915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7431572
X-RAY DIFFRACTIONr_chiral_restr0.0810.21719
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211429
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022024
X-RAY DIFFRACTIONr_nbd_refined0.2010.22332
X-RAY DIFFRACTIONr_nbd_other0.1870.210536
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25152
X-RAY DIFFRACTIONr_nbtor_other0.0850.25908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2430
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3161.58469
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.445210468
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94934858
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8524.54055
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2550tight positional0.030.05
12B2550tight positional0.030.05
13C2550tight positional0.030.05
14D2550tight positional0.030.05
15E2550tight positional0.040.05
16F2550tight positional0.030.05
21A1tight positional00.05
11A46loose positional0.265
12B46loose positional0.295
13C46loose positional0.525
14D46loose positional0.325
15E46loose positional0.695
16F46loose positional0.465
11A2550tight thermal0.20.5
12B2550tight thermal0.150.5
13C2550tight thermal0.150.5
14D2550tight thermal0.160.5
15E2550tight thermal0.180.5
16F2550tight thermal0.130.5
21A1tight thermal0.380.5
11A46loose thermal7.2410
12B46loose thermal7.1110
13C46loose thermal7.7910
14D46loose thermal11.4810
15E46loose thermal3.0210
16F46loose thermal7.2310
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 312
Rwork0.27 5977

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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