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- PDB-2fah: The structure of mitochondrial PEPCK, Complex with Mn and GDP -

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Basic information

Entry
Database: PDB / ID: 2fah
TitleThe structure of mitochondrial PEPCK, Complex with Mn and GDP
ComponentsPhosphoenolpyruvate carboxykinase
KeywordsLYASE / phosphoenolpyruvate carboxykinase / PEPCK / PCK / PEP / GDP / kinase / phosphoryl transfer
Function / homology
Function and homology information


eggshell formation / lactate oxidation / egg-laying behavior / regulation of viral process / Gluconeogenesis / glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / embryonic organ morphogenesis ...eggshell formation / lactate oxidation / egg-laying behavior / regulation of viral process / Gluconeogenesis / glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / embryonic organ morphogenesis / vitellogenesis / lactate metabolic process / glycerol catabolic process / hepatocyte differentiation / pyruvate metabolic process / cellular response to ethanol / glucose catabolic process to lactate via pyruvate / embryo development ending in birth or egg hatching / regulation of gluconeogenesis / response to starvation / response to cAMP / cellular response to dexamethasone stimulus / gluconeogenesis / cellular response to glucose stimulus / cellular response to insulin stimulus / manganese ion binding / mitochondrial matrix / GTP binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 ...Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
octanoyl-sucrose, esterificated at glucose C6 / GUANOSINE-5'-DIPHOSPHATE / MALONIC ACID / : / Phosphoenolpyruvate carboxykinase [GTP], mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsHolyoak, T. / Sullivan, S.M. / Nowak, T.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Insights into the Mechanism of PEPCK Catalysis
Authors: Holyoak, T. / Sullivan, S.M. / Nowak, T.
History
DepositionDec 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999Sequence The changes in the protein sequence represent errors in the original published sequence. ...Sequence The changes in the protein sequence represent errors in the original published sequence. These changes were verified by resequencing of the gene and mass spectrometry analysis.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase
B: Phosphoenolpyruvate carboxykinase
C: Phosphoenolpyruvate carboxykinase
D: Phosphoenolpyruvate carboxykinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,23723
Polymers269,5684
Non-polymers3,67019
Water26,1221450
1
A: Phosphoenolpyruvate carboxykinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0495
Polymers67,3921
Non-polymers6574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoenolpyruvate carboxykinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1536
Polymers67,3921
Non-polymers7615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphoenolpyruvate carboxykinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5186
Polymers67,3921
Non-polymers1,1265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphoenolpyruvate carboxykinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5186
Polymers67,3921
Non-polymers1,1265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.595, 90.852, 103.339
Angle α, β, γ (deg.)64.23, 73.74, 71.18
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D
331A
341B
351C
361D
371A
381B
391C
401D
411A
421B
431C
441D
451A
461B
471C
481D
491A
501B
511C
521D
531A
541B
551C
561D
571A
581B
591C
601D
611A
621B
631C
641D
651A
661B
671C
681D
691A
701B
711C
721D
731A
741B
751C
761D
771A
781B
791C
801D
811A
821B
831C
841D
851A
861B
871C
881D
891A
901B
911C
921D
931A
941B
951C
961D
971A
981B
991C
1001D
1011A
1021B
1031C
1041D
1051A
1061B
1071C
1081D
1091A
1101B
1111C
1121D
1131A
1141B
1151C
1161D
1171A
1181B
1191C
1201D
1211A
1221B
1231C
1241D
1251A
1261B
1271C
1281D
1291A
1301B
1311C
1321D
1331A
1341B
1351C
1361D

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
11LEULEUGLNGLN1AA74 - 7941 - 46
21LEULEUGLNGLN1BB74 - 7941 - 46
31LEULEUGLNGLN1CC74 - 7941 - 46
41LEULEUGLNGLN1DD74 - 7941 - 46
52VALVALSERSER1AA61 - 6728 - 34
62VALVALSERSER1BB61 - 6728 - 34
72VALVALSERSER1CC61 - 6728 - 34
82VALVALSERSER1DD61 - 6728 - 34
93LEULEUPROPRO1AA55 - 5822 - 25
103LEULEUPROPRO1BB55 - 5822 - 25
113LEULEUPROPRO1CC55 - 5822 - 25
123LEULEUPROPRO1DD55 - 5822 - 25
134ALAALAVALVAL1AA144 - 146111 - 113
144ALAALAVALVAL1BB144 - 146111 - 113
154ALAALAVALVAL1CC144 - 146111 - 113
164ALAALAVALVAL1DD144 - 146111 - 113
175GLUGLUMETMET1AA148 - 166115 - 133
185GLUGLUMETMET1BB148 - 166115 - 133
195GLUGLUMETMET1CC148 - 166115 - 133
205GLUGLUMETMET1DD148 - 166115 - 133
216GLYGLYTHRTHR1AA177 - 194144 - 161
226GLYGLYTHRTHR1BB177 - 194144 - 161
236GLYGLYTHRTHR1CC177 - 194144 - 161
246GLYGLYTHRTHR1DD177 - 194144 - 161
257LEULEUGLUGLU1AA221 - 244188 - 211
267LEULEUGLUGLU1BB221 - 244188 - 211
277LEULEUGLUGLU1CC221 - 244188 - 211
287LEULEUGLUGLU1DD221 - 244188 - 211
298TRPTRPASPASP1AA322 - 337289 - 304
308TRPTRPASPASP1BB322 - 337289 - 304
318TRPTRPASPASP1CC322 - 337289 - 304
328TRPTRPASPASP1DD322 - 337289 - 304
339PROPROARGARG1AA528 - 538495 - 505
349PROPROARGARG1BB528 - 538495 - 505
359PROPROARGARG1CC528 - 538495 - 505
369PROPROARGARG1DD528 - 538495 - 505
3710TRPTRPASPASP1AA439 - 441406 - 408
3810TRPTRPASPASP1BB439 - 441406 - 408
3910TRPTRPASPASP1CC439 - 441406 - 408
4010TRPTRPASPASP1DD439 - 441406 - 408
4111GLYGLYPROPRO1AA444 - 457411 - 424
4211GLYGLYPROPRO1BB444 - 457411 - 424
4311GLYGLYPROPRO1CC444 - 457411 - 424
4411GLYGLYPROPRO1DD444 - 457411 - 424
4512GLYGLYTRPTRP1AA459 - 469426 - 436
4612GLYGLYTRPTRP1BB459 - 469426 - 436
4712GLYGLYTRPTRP1CC459 - 469426 - 436
4812GLYGLYTRPTRP1DD459 - 469426 - 436
4913HISHISSERSER1AA471 - 481438 - 448
5013HISHISSERSER1BB471 - 481438 - 448
5113HISHISSERSER1CC471 - 481438 - 448
5213HISHISSERSER1DD471 - 481438 - 448
5314ALAALAHISHIS1AA483 - 489450 - 456
5414ALAALAHISHIS1BB483 - 489450 - 456
5514ALAALAHISHIS1CC483 - 489450 - 456
5614ALAALAHISHIS1DD483 - 489450 - 456
5715METMETLEULEU1AA495 - 521462 - 488
5815METMETLEULEU1BB495 - 521462 - 488
5915METMETLEULEU1CC495 - 521462 - 488
6015METMETLEULEU1DD495 - 521462 - 488
6116PHEPHEILEILE1AA544 - 559511 - 526
6216PHEPHEILEILE1BB544 - 559511 - 526
6316PHEPHEILEILE1CC544 - 559511 - 526
6416PHEPHEILEILE1DD544 - 559511 - 526
6517LYSLYSARGARG1AA601 - 612568 - 579
6617LYSLYSARGARG1BB601 - 612568 - 579
6717LYSLYSARGARG1CC601 - 612568 - 579
6817LYSLYSARGARG1DD601 - 612568 - 579
6918TYRTYRGLUGLU1AA614 - 635581 - 602
7018TYRTYRGLUGLU1BB614 - 635581 - 602
7118TYRTYRGLUGLU1CC614 - 635581 - 602
7218TYRTYRGLUGLU1DD614 - 635581 - 602
7319LEULEUSERSER1AA34 - 371 - 4
7419LEULEUSERSER1BB34 - 371 - 4
7519LEULEUSERSER1CC34 - 371 - 4
7619LEULEUSERSER1DD34 - 371 - 4
7720GLUGLULYSLYS1AA69 - 7236 - 39
7820GLUGLULYSLYS1BB69 - 7236 - 39
7920GLUGLULYSLYS1CC69 - 7236 - 39
8020GLUGLULYSLYS1DD69 - 7236 - 39
8121ASPASPPROPRO1AA81 - 8848 - 55
8221ASPASPPROPRO1BB81 - 8848 - 55
8321ASPASPPROPRO1CC81 - 8848 - 55
8421ASPASPPROPRO1DD81 - 8848 - 55
8522TYRTYRTHRTHR1AA90 - 11457 - 81
8622TYRTYRTHRTHR1BB90 - 11457 - 81
8722TYRTYRTHRTHR1CC90 - 11457 - 81
8822TYRTYRTHRTHR1DD90 - 11457 - 81
8923ALAALAPHEPHE1AA120 - 14287 - 109
9023ALAALAPHEPHE1BB120 - 14287 - 109
9123ALAALAPHEPHE1CC120 - 14287 - 109
9223ALAALAPHEPHE1DD120 - 14287 - 109
9324ARGARGSERSER1AA246 - 271213 - 238
9424ARGARGSERSER1BB246 - 271213 - 238
9524ARGARGSERSER1CC246 - 271213 - 238
9624ARGARGSERSER1DD246 - 271213 - 238
9725METMETLEULEU1AA273 - 319240 - 286
9825METMETLEULEU1BB273 - 319240 - 286
9925METMETLEULEU1CC273 - 319240 - 286
10025METMETLEULEU1DD273 - 319240 - 286
10126SERSERTRPTRP1AA383 - 405350 - 372
10226SERSERTRPTRP1BB383 - 405350 - 372
10326SERSERTRPTRP1CC383 - 405350 - 372
10426SERSERTRPTRP1DD383 - 405350 - 372
10527ASPASPLYSLYS1AA567 - 579534 - 546
10627ASPASPLYSLYS1BB567 - 579534 - 546
10727ASPASPLYSLYS1CC567 - 579534 - 546
10827ASPASPLYSLYS1DD567 - 579534 - 546
10928LEULEUPROPRO1AA596 - 598563 - 565
11028LEULEUPROPRO1BB596 - 598563 - 565
11128LEULEUPROPRO1CC596 - 598563 - 565
11228LEULEUPROPRO1DD596 - 598563 - 565
11329PHEPHELEULEU1AA208 - 219175 - 186
11429PHEPHELEULEU1BB208 - 219175 - 186
11529PHEPHELEULEU1CC208 - 219175 - 186
11629PHEPHELEULEU1DD208 - 219175 - 186
11730LEULEULEULEU1AA342 - 381309 - 348
11830LEULEULEULEU1BB342 - 381309 - 348
11930LEULEULEULEU1CC342 - 381309 - 348
12030LEULEULEULEU1DD342 - 381309 - 348
12131CYSCYSPROPRO4AA418 - 437385 - 404
12231CYSCYSPROPRO4BB418 - 437385 - 404
12331CYSCYSPROPRO4CC418 - 437385 - 404
12431CYSCYSPROPRO4DD418 - 437385 - 404
12532GLYGLYGLYGLY4AA561 - 565528 - 532
12632GLYGLYGLYGLY4BB561 - 565528 - 532
12732GLYGLYGLYGLY4CC561 - 565528 - 532
12832GLYGLYGLYGLY4DD561 - 565528 - 532
12933ASPASPSERSER1AA582 - 594549 - 561
13033ASPASPSERSER1BB582 - 594549 - 561
13133ASPASPSERSER1CC582 - 594549 - 561
13233ASPASPSERSER1DD582 - 594549 - 561
13334GLUGLUGLYGLY4AA580 - 581547 - 548
13434GLUGLUGLYGLY4BB580 - 581547 - 548
13534GLUGLUGLYGLY4CC580 - 581547 - 548
13634GLUGLUGLYGLY4DD580 - 581547 - 548
Detailsbiological unit is a monomer

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

#1: Protein
Phosphoenolpyruvate carboxykinase / / Phosphoenolpyruvate carboxylase / PEPCK-M


Mass: 67391.883 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: liver mitochondrial isozyme / Source: (natural) Gallus gallus (chicken)
References: UniProt: P21642, phosphoenolpyruvate carboxykinase (GTP)
#2: Polysaccharide beta-D-fructofuranose-(2-1)-6-O-octanoyl-alpha-D-glucopyranose / octanoyl-sucrose / esterificated at glucose C6


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 468.493 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: octanoyl-sucrose, esterificated at glucose C6
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5_6*OCCCCCCCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1467 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1450 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 16% PEG6000, 0.1M HEPES, n-octanoylsucrose, GDP, MnCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 20, 2005 / Details: Blue osmic, confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→100 Å / Num. obs: 127447 / % possible obs: 95.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.106
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.09-2.1830.581191.9
2.18-2.2630.457192.2
2.26-2.372.90.384193.3
2.37-2.493.10.327193.9
2.49-2.653.10.268195.1
2.65-2.853.20.192195.8
2.85-3.143.30.135196.6
3.14-3.593.50.097197.2
3.59-4.523.70.066198
4.52-1003.70.045198.8

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Phasing

Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2FAG

2fag
PDB Unreleased entry


Resolution: 2.09→32.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.098 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23366 6402 5 %RANDOM
Rwork0.18673 ---
obs0.1891 120981 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.194 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0.18 Å2-1.16 Å2
2--0.67 Å2-0.48 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.09→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18901 0 219 1450 20570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02219927
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.97527190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26452497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.06222.225899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.063153048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.34515210
X-RAY DIFFRACTIONr_chiral_restr0.0820.22803
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215738
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.29807
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.213299
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.21615
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.2234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.281
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3681.512574
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.539219762
X-RAY DIFFRACTIONr_scbond_it1.01738492
X-RAY DIFFRACTIONr_scangle_it1.6624.57396
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
1A3488tight positional0.060.05
2B3488tight positional0.050.05
3C3488tight positional0.060.05
4D3488tight positional0.050.05
1A192medium positional0.190.5
2B192medium positional0.20.5
3C192medium positional0.20.5
4D192medium positional0.270.5
1A3488tight thermal0.10.5
2B3488tight thermal0.10.5
3C3488tight thermal0.110.5
4D3488tight thermal0.10.5
1A192medium thermal0.612
2B192medium thermal0.582
3C192medium thermal0.622
4D192medium thermal0.552
LS refinement shellResolution: 2.093→2.147 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 395 -
Rwork0.251 8000 -
obs--84.33 %
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)
14.47451.35130.65261.2840.12050.1019-0.06460.1052-0.6364-0.0272-0.0674-0.48210.59880.22150.1320.28770.1270.0968-0.05520.04940.035637.164523.04284.2375
21.4159-1.1395-0.09564.021.11580.3542-0.2137-0.42670.06660.5020.1175-0.08730.24370.21020.09620.2250.15640.06060.13130.0519-0.049834.551936.404718.8693
30.98110.17540.31790.88540.77892.1174-0.040.1180.0737-0.094-0.0159-0.0421-0.13870.1050.0559-0.00480.04750.1109-0.10640.0395-0.033931.909944.1012-5.3345
42.7389-1.8654-1.20372.84140.47654.4745-0.0375-0.1686-0.40870.06970.0110.37160.4002-0.15490.02650.08690.07060.1042-0.14220.0608-0.059925.845931.57527.7911
52.32260.5620.96113.06131.11733.60570.0794-0.1038-0.21280.11580.0407-0.07940.30260.1108-0.1201-0.02340.10110.1055-0.08480.0407-0.046534.657236.89632.5333
64.1075-0.0896-0.17261.323-1.85494.28710.0357-0.00280.02110.0273-0.01690.14480.3529-0.0808-0.01880.0140.06960.0975-0.10780.0221-0.094829.013739.2385-0.2931
713.86336.75789.82077.58217.32328.93360.03880.2775-0.6409-0.43090.0652-0.17730.6040.2478-0.1040.04330.040.1208-0.09360.0246-0.078418.271833.6282-8.7746
82.2751-1.1682-1.46581.2082-0.05412.0799-0.0184-0.0521-0.12170.1016-0.04490.09490.1034-0.17890.0632-0.00480.01580.0885-0.07420.0283-0.07664.569940.8663.8865
92.6730.6381.55371.71361.44791.64610.063-0.41840.30470.2334-0.0710.01690.0058-0.22990.0080.03630.03050.1064-0.00690.0192-0.067118.346651.527818.3933
106.69992.12096.7593.31772.7759.8069-0.2909-0.78170.96790.3969-0.22270.0443-0.7988-0.58130.51360.12990.07920.04750.0219-0.10880.129226.535661.42219.5191
111.371-0.44080.39690.36960.43031.48020.041-0.02220.0804-0.0064-0.01720.01810.0288-0.0104-0.02380.00770.02180.0894-0.12390.0101-0.057310.38547.7371-2.6775
125.63990.9142-0.18243.2208-0.14572.59670.0722-0.0634-0.4291-0.1654-0.11610.16990.30130.08610.04390.04890.0420.0727-0.1050.0075-0.06543.707737.8024-13.7072
136.66375.23631.86298.14650.80157.36680.3359-0.23370.63350.2836-0.3639-0.1673-1.0890.01390.02810.11990.03320.1262-0.03460.01570.01765.632262.71990.722
141.2649-0.26640.24642.6721-0.20923.3262-0.008-0.07820.1447-0.0131-0.06790.2954-0.0677-0.33990.0759-0.02840.03680.0978-0.05350.0142-0.0639-5.373654.0903-0.1982
151.6154-0.4614-0.2521.37060.00973.49250.20120.10690.3131-0.085-0.1532-0.0436-0.3301-0.2034-0.0480.03340.01380.0736-0.06720.04160.00882.91258.9488-13.8269
161.4096-1.64910.26033.4197-0.81461.4838-0.315-0.3566-0.02170.52390.2158-0.33160.04240.07250.09920.09760.08070.01720.04690.01330.041115.453-10.908711.8966
174.1479-1.43361.08643.7862-1.32982.89760.2630.170.2492-0.3956-0.2185-0.32090.07030.3189-0.04440.01120.06610.1704-0.03450.03690.013914.8665-0.5932-16.5277
181.43630.0768-0.81332.5033-1.09371.7025-0.0908-0.089-0.1706-0.05810.06310.07180.089-0.00630.02770.05830.06270.0797-0.06740.0437-0.0259.6905-14.3064.4972
198.0001-0.7858-0.41884.7541-2.07742.9128-0.0678-0.453-0.206-0.3932-0.1651-0.56460.1030.08510.23280.01770.15560.137-0.01540.1175-0.040218.5793-11.63910.7367
203.3453-0.33571.35714.841.33627.8334-0.02580.08580.01660.13950.0867-0.4794-0.01250.3001-0.0609-0.04850.06470.0903-0.09210.0354-0.004117.8989-4.1741-2.1085
214.6096-0.39820.82361.2965-0.82990.6826-0.0239-0.2359-0.2014-0.08190.12960.06040.1424-0.0313-0.10570.02130.03490.1061-0.09220.0559-0.0527-0.7062-4.8724-3.6921
223.5167-0.92681.27072.4706-0.01412.2113-0.2069-0.8281-0.39860.24840.25950.30.0413-0.3859-0.05260.05310.10240.12170.08850.1211-0.0062-12.9357-0.08542.4461
231.80011.39182.29985.71452.64534.0661-0.2458-0.6844-0.13290.40160.19720.2377-0.1896-0.6480.04860.07060.15360.15040.18290.1167-0.0584-6.526-0.57678.0391
245.4375-1.58280.22736.3397-0.68266.645-0.4518-0.94990.18650.90190.4015-0.3784-0.8112-0.3690.05030.33330.2037-0.05220.1791-0.0519-0.07515.65255.909619.9076
255.04470.1863-0.78282.4916-0.7994.2909-0.1652-0.92970.71861.11730.2845-0.2709-1.0895-0.0118-0.11920.53350.2127-0.06870.2046-0.15720.08257.678612.623318.3365
2613.89012.1749.88985.01471.955428.00720.4015-0.0031-0.97510.3420.54060.24191.4949-0.1791-0.9420.20130.14540.10680.28260.25420.2069-11.0345-8.374910.2387
272.3517-1.66350.4561.5766-0.30051.54620.0232-0.0254-0.0079-0.1002-0.02750.00510.0204-0.03580.0044-0.00010.03980.0994-0.08960.0369-0.0923-7.3924.8013-10.8164
284.8991-1.44291.0292.1825-0.90174.1141-0.3375-0.65480.25830.14770.237-0.0344-0.3105-0.25210.10050.00520.12590.08840.035-0.019-0.094-18.217514.47-1.9775
294.3045-1.9785-1.36313.09010.36194.11880.0894-0.07530.6094-0.0369-0.0417-0.2328-0.4072-0.1449-0.04770.00470.00330.0081-0.09180.0005-0.017-10.587618.0771-11.8019
307.9764-5.3033-1.935425.14752.65126.05660.29030.66790.2133-0.9958-0.38320.4403-0.2323-0.28310.09290.01620.02380.02530.03460.0649-0.0948-13.101414.704-24.1666
313.420.0917-1.19051.6967-0.27813.72080.0940.20880.236-0.1187-0.04890.1162-0.3609-0.2442-0.04510.07370.05930.0452-0.06140.0523-0.071949.85760.327723.5565
321.6531-0.32270.09050.64730.29441.3720.0236-0.0099-0.03790.0102-0.022-0.0013-0.0280.0826-0.00160.03250.00930.099-0.13530.0444-0.117759.283850.170233.2403
333.6739-0.39040.87632.0020.34423.0862-0.14930.16520.1635-0.33810.0380.1275-0.2084-0.01240.11130.01850.02440.1063-0.0770.0684-0.145756.094251.884527.4596
343.38332.20982.70651.78142.00523.2839-0.13680.32990.1954-0.06530.1693-0.1196-0.16130.3171-0.03240.03740.02490.1293-0.09580.0412-0.043865.997754.35336.9346
351.0066-1.3158-0.97521.8080.80543.4476-0.0341-0.12440.18940.14520.09530.0039-0.14250.0357-0.06120.01530.02510.0855-0.10890.0187-0.074558.86959.542257.3437
361.00990.80830.40122.32861.0374.00350.0046-0.16290.16030.0616-0.09750.4286-0.1186-0.44890.0929-0.01620.00980.1182-0.0616-0.0102-0.005440.900650.003348.3067
379.89852.1056-0.92425.82564.592913.29760.2105-0.6606-0.06040.4338-0.67480.90770.3739-1.43680.46430.132-0.13020.14590.12930.00030.101333.374840.053746.6911
381.4403-0.55980.70370.31560.162.2599-0.0215-0.03770.0086-0.00150.01960.0489-0.007-0.04970.0019-0.00940.00920.1481-0.11380.0424-0.079953.868551.628453.6926
392.64643.51850.90785.6393-3.746325.83540.1278-0.2709-0.04030.078-0.0977-0.4523-0.230.6051-0.0301-0.00360.08590.1036-0.08930.0375-0.082575.715150.985863.7365
402.0836-0.69310.20390.8742-0.32062.6653-0.0209-0.0595-0.18080.0139-0.0058-0.09220.22850.07990.02670.00250.05840.1051-0.08010.0247-0.119469.620244.699949.8493
4113.26710.5554-3.168.9522.632513.39410.0022-0.34311.9824-0.42180.2572-1.2344-1.8181.4604-0.25940.1783-0.06440.09120.12890.02740.374875.076562.467261.7495
423.54811.6294-0.07743.2454-0.14871.6823-0.0737-0.0082-0.05650.12340.03090.04550.2269-0.04860.04270.00340.04380.1229-0.10930.0344-0.15257.112546.302466.7748
437.99620.7897-0.03691.3544-0.42992.1274-0.0734-0.5236-0.35290.47290.05660.19940.2092-0.10510.01680.09640.05360.0895-0.03150.0453-0.067662.166145.229475.2748
444.59843.6834-7.85043.9325-7.404420.9011-0.2548-0.0631-0.462-0.2754-0.1395-0.24311.06990.73580.39430.05450.1140.0787-0.05920.0109-0.035976.164834.920256.9069
452.91140.8301-0.59517.6892-4.19157.9624-0.0515-0.0863-0.20230.00020.0779-0.07420.23750.5322-0.02640.00090.09410.0491-0.0354-0.0163-0.050381.329140.428363.8929
462.596-0.3768-0.73841.5389-0.59232.05320.18780.50550.4229-0.2424-0.05020.1903-0.1086-0.0714-0.13750.16450.07550.06530.0170.08380.035166.5905101.489729.956
474.8404-1.62713.34411.1826-2.40864.9060.26450.4888-0.2094-0.3337-0.19580.00440.43940.4875-0.06870.21760.1630.13890.0688-0.0196-0.061487.070786.840531.0873
483.04060.7125-0.55284.4492-0.53131.4130.1088-0.01150.52250.0214-0.0574-0.2972-0.29220.1559-0.05140.11430.05550.1601-0.05550.07440.082274.652107.089236.5984
494.4802-0.1866-0.3923.3155-1.28576.24660.16990.12430.1004-0.4453-0.25-0.33710.08490.11580.08010.07890.25040.20080.06840.1507-0.036276.13598.614327.0876
5010.37780.72741.76532.8149-0.33894.03050.07110.5191-0.1424-0.3743-0.03520.0230.3710.3361-0.03590.1670.13950.13460.03370.0437-0.144876.426690.625529.8664
5111.59374.59065.37243.04832.41073.9686-0.06020.22020.481-0.0873-0.10990.0348-0.10570.14770.17010.10590.08760.1526-0.05760.0503-0.037482.758796.863340.8813
522.5928-1.2864-2.21131.69680.50273.1375-0.02-0.07460.0790.03520.01420.1176-0.08760.03520.00580.03810.06330.0855-0.0730.0243-0.081577.063999.514559.2685
532.3559-0.4527-0.611.00750.78043.9972-0.1267-0.01020.25660.08930.09490.0608-0.2314-0.02060.03170.130.08850.0775-0.11810.02590.021578.7442104.802157.6585
542.94890.43561.90542.93061.07582.4447-0.0727-0.31960.0507-0.00460.00130.3419-0.1238-0.23470.07150.05760.05590.1302-0.08120.03340.033958.379894.774649.3244
554.4629-1.4083-1.9837.4214.0557.9211-0.2498-0.1519-0.14660.3766-0.1881.08750.4147-0.96430.43770.1731-0.03350.08580.04610.05330.215649.508585.328946.5889
561.3525-0.5981.34580.55670.30334.1003-0.1652-0.0680.1327-0.10130.13970.0935-0.21940.03580.02550.02440.07810.1584-0.08220.01820.067566.192199.080550.2056
571.3232-0.8491-0.21211.14060.361.560.00750.0019-0.0780.0006-0.0410.0560.0416-0.08390.03350.02610.05460.1234-0.07660.0352-0.05983.567989.476660.5286
582.331-0.54790.51642.15371.20084.39870.10250.07670.0758-0.0924-0.1562-0.10160.08140.02660.05370.03610.10790.1464-0.0550.0866-0.09389.295991.105652.4809
592.43340.23950.22172.37320.06651.21860.0547-0.1644-0.06240.2544-0.12180.0810.0925-0.09810.06710.03860.02970.1329-0.05840.0249-0.076275.858387.837371.5372
601.95360.3742-0.46512.5544-1.20055.91530.08630.0213-0.28860.1067-0.0604-0.14080.39840.0934-0.02590.09380.12970.0936-0.01250.01680.020293.617277.541661.3185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA34 - 561 - 23
2X-RAY DIFFRACTION2AA57 - 8924 - 56
3X-RAY DIFFRACTION3AA90 - 15757 - 124
4X-RAY DIFFRACTION4AA158 - 196125 - 163
5X-RAY DIFFRACTION5AA197 - 243164 - 210
6X-RAY DIFFRACTION6AA244 - 264211 - 231
7X-RAY DIFFRACTION7AA265 - 278232 - 245
8X-RAY DIFFRACTION8AA279 - 349246 - 316
9X-RAY DIFFRACTION9AA350 - 393317 - 360
10X-RAY DIFFRACTION10AA394 - 423361 - 390
11X-RAY DIFFRACTION11AA424 - 510391 - 477
12X-RAY DIFFRACTION12AA511 - 530478 - 497
13X-RAY DIFFRACTION13AA531 - 543498 - 510
14X-RAY DIFFRACTION14AA544 - 579511 - 546
15X-RAY DIFFRACTION15AA580 - 641547 - 608
16X-RAY DIFFRACTION16BB34 - 1061 - 73
17X-RAY DIFFRACTION17BB107 - 14874 - 115
18X-RAY DIFFRACTION18BB149 - 203116 - 170
19X-RAY DIFFRACTION19BB204 - 223171 - 190
20X-RAY DIFFRACTION20BB224 - 249191 - 216
21X-RAY DIFFRACTION21BB250 - 294217 - 261
22X-RAY DIFFRACTION22BB295 - 338262 - 305
23X-RAY DIFFRACTION23BB339 - 371306 - 338
24X-RAY DIFFRACTION24BB372 - 390339 - 357
25X-RAY DIFFRACTION25BB391 - 429358 - 396
26X-RAY DIFFRACTION26BB430 - 441397 - 408
27X-RAY DIFFRACTION27BB442 - 531409 - 498
28X-RAY DIFFRACTION28BB532 - 580499 - 547
29X-RAY DIFFRACTION29BB581 - 624548 - 591
30X-RAY DIFFRACTION30BB625 - 641592 - 608
31X-RAY DIFFRACTION31CC34 - 851 - 52
32X-RAY DIFFRACTION32CC86 - 19553 - 162
33X-RAY DIFFRACTION33CC196 - 241163 - 208
34X-RAY DIFFRACTION34CC242 - 280209 - 247
35X-RAY DIFFRACTION35CC281 - 350248 - 317
36X-RAY DIFFRACTION36CC351 - 389318 - 356
37X-RAY DIFFRACTION37CC390 - 411357 - 378
38X-RAY DIFFRACTION38CC412 - 464379 - 431
39X-RAY DIFFRACTION39CC465 - 473432 - 440
40X-RAY DIFFRACTION40CC474 - 521441 - 488
41X-RAY DIFFRACTION41CC522 - 530489 - 497
42X-RAY DIFFRACTION42CC531 - 565498 - 532
43X-RAY DIFFRACTION43CC566 - 600533 - 567
44X-RAY DIFFRACTION44CC601 - 622568 - 589
45X-RAY DIFFRACTION45CC623 - 641590 - 608
46X-RAY DIFFRACTION46DD34 - 1081 - 75
47X-RAY DIFFRACTION47DD109 - 15976 - 126
48X-RAY DIFFRACTION48DD160 - 202127 - 169
49X-RAY DIFFRACTION49DD203 - 223170 - 190
50X-RAY DIFFRACTION50DD224 - 253191 - 220
51X-RAY DIFFRACTION51DD254 - 277221 - 244
52X-RAY DIFFRACTION52DD278 - 316245 - 283
53X-RAY DIFFRACTION53DD317 - 350284 - 317
54X-RAY DIFFRACTION54DD351 - 391318 - 358
55X-RAY DIFFRACTION55DD392 - 414359 - 381
56X-RAY DIFFRACTION56DD415 - 441382 - 408
57X-RAY DIFFRACTION57DD442 - 487409 - 454
58X-RAY DIFFRACTION58DD488 - 529455 - 496
59X-RAY DIFFRACTION59DD530 - 598497 - 565
60X-RAY DIFFRACTION60DD599 - 641566 - 608

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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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