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- PDB-5mrw: Structure of the KdpFABC complex -

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Basic information

Entry
Database: PDB / ID: 5mrw
TitleStructure of the KdpFABC complex
Components(Potassium-transporting ATPase ...) x 4
KeywordsHYDROLASE / membrane protein complex potassium transport P-type ATPase SKT channel
Function / homology
Function and homology information


plasma membrane => GO:0005886 / P-type K+ transporter / P-type potassium transmembrane transporter activity / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / monoatomic cation transmembrane transport / potassium ion binding / potassium ion transmembrane transport / potassium ion transport / hydrolase activity ...plasma membrane => GO:0005886 / P-type K+ transporter / P-type potassium transmembrane transporter activity / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / monoatomic cation transmembrane transport / potassium ion binding / potassium ion transmembrane transport / potassium ion transport / hydrolase activity / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Potassium-transporting ATPase C chain / Potassium-transporting ATPase A chain / K+ transporting P-type ATPase, F subunit / K+-transporting ATPase, c chain / Potassium-transporting ATPase A subunit / F subunit of K+-transporting ATPase (Potass_KdpF) / P-type ATPase, B chain, subfamily IA / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / E1-E2 ATPase ...Potassium-transporting ATPase C chain / Potassium-transporting ATPase A chain / K+ transporting P-type ATPase, F subunit / K+-transporting ATPase, c chain / Potassium-transporting ATPase A subunit / F subunit of K+-transporting ATPase (Potass_KdpF) / P-type ATPase, B chain, subfamily IA / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Potassium-transporting ATPase KdpC subunit / Potassium-transporting ATPase potassium-binding subunit / Potassium-transporting ATPase ATP-binding subunit / Potassium-transporting ATPase KdpC subunit / Potassium-transporting ATPase KdpF subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsHuang, C. / Pedersen, B.P. / Stokes, D.L.
Funding support United States, Denmark, 3items
OrganizationGrant numberCountry
National Institutes of HealthGM108043 United States
Danish Council for Independent ResearchDFF-4002-00052 Denmark
European Research Council637372 Denmark
CitationJournal: Nature / Year: 2017
Title: Crystal structure of the potassium-importing KdpFABC membrane complex.
Authors: Huang, C.S. / Pedersen, B.P. / Stokes, D.L.
History
DepositionDec 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
Revision 1.2Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 13, 2024Group: 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_entry_details / pdbx_modification_feature / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium-transporting ATPase potassium-binding subunit
B: Potassium-transporting ATPase ATP-binding subunit
C: Potassium-transporting ATPase KdpC subunit
D: Potassium-transporting ATPase KdpF subunit
E: Potassium-transporting ATPase potassium-binding subunit
F: Potassium-transporting ATPase ATP-binding subunit
G: Potassium-transporting ATPase KdpC subunit
H: Potassium-transporting ATPase KdpF subunit
I: Potassium-transporting ATPase potassium-binding subunit
J: Potassium-transporting ATPase ATP-binding subunit
K: Potassium-transporting ATPase KdpC subunit
L: Potassium-transporting ATPase KdpF subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,93425
Polymers460,57412
Non-polymers5,36013
Water543
1
A: Potassium-transporting ATPase potassium-binding subunit
B: Potassium-transporting ATPase ATP-binding subunit
C: Potassium-transporting ATPase KdpC subunit
D: Potassium-transporting ATPase KdpF subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,5069
Polymers153,5254
Non-polymers1,9825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17310 Å2
ΔGint-133 kcal/mol
Surface area52740 Å2
MethodPISA
2
E: Potassium-transporting ATPase potassium-binding subunit
F: Potassium-transporting ATPase ATP-binding subunit
G: Potassium-transporting ATPase KdpC subunit
H: Potassium-transporting ATPase KdpF subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,2148
Polymers153,5254
Non-polymers1,6894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-138 kcal/mol
Surface area52780 Å2
MethodPISA
3
I: Potassium-transporting ATPase potassium-binding subunit
J: Potassium-transporting ATPase ATP-binding subunit
K: Potassium-transporting ATPase KdpC subunit
L: Potassium-transporting ATPase KdpF subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,2148
Polymers153,5254
Non-polymers1,6894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16590 Å2
ΔGint-135 kcal/mol
Surface area53340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.720, 166.290, 196.300
Angle α, β, γ (deg.)90.000, 107.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain D
21chain H
31chain L
12(chain A and (resseq 1:54 or resseq 56:57 or (resid...
22(chain E and (resseq 1:54 or resseq 56:57 or (resid...
32(chain I and (resseq 1:54 or resseq 56:57 or (resid...
13(chain G and (resseq 4:7 or (resid 8 and (name...
23(chain C and (resseq 4:7 or (resid 8 and (name...
33(chain K and (resseq 4:7 or (resid 8 and (name...
14(chain F and (resseq 9:77 or (resid 78 and (name...
24(chain B and (resseq 9:77 or (resid 78 and (name...
34(chain J and (resseq 9:77 or (resid 78 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLUGLUchain DDD1 - 271 - 27
211METMETGLUGLUchain HHH1 - 271 - 27
311METMETGLUGLUchain LLL1 - 271 - 27
112METMETASPASP(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 541 - 54
122GLUGLUMETMET(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA56 - 5756 - 57
132ASNASNASNASN(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA5858
142METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
152METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
162METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
172METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
182METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
192METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
212METMETASPASP(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 541 - 54
222GLUGLUMETMET(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE56 - 5756 - 57
232ASNASNASNASN(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE5858
242METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
252METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
262METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
272METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
282METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
292METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
312METMETASPASP(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 541 - 54
322GLUGLUMETMET(chain I and (resseq 1:54 or resseq 56:57 or (resid...II56 - 5756 - 57
332ASNASNASNASN(chain I and (resseq 1:54 or resseq 56:57 or (resid...II5858
342METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
352METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
362METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
372METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
382METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
392METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
113LEULEUALAALA(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 71 - 4
123LEULEULEULEU(chain G and (resseq 4:7 or (resid 8 and (name...GG85
133LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
143LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
153LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
163LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
173LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
183LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
213LEULEUALAALA(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 71 - 4
223LEULEULEULEU(chain C and (resseq 4:7 or (resid 8 and (name...CC85
233LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
243LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
253LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
263LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
273LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
283LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
313LEULEUALAALA(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 71 - 4
323LEULEULEULEU(chain K and (resseq 4:7 or (resid 8 and (name...KK85
333LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
343LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
353LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
363LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
373LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
383LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
114PHEPHELEULEU(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 771 - 69
124PHEPHEPHEPHE(chain F and (resseq 9:77 or (resid 78 and (name...FF7870
134PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
144PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
154PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
164PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
174PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
184PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
194PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
1104PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
214PHEPHELEULEU(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 771 - 69
224PHEPHEPHEPHE(chain B and (resseq 9:77 or (resid 78 and (name...BB7870
234PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
244PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
254PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
264PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
274PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
284PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
294PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
2104PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
314PHEPHELEULEU(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 771 - 69
324PHEPHEPHEPHE(chain J and (resseq 9:77 or (resid 78 and (name...JJ7870
334PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
344PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
354PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
364PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
374PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
384PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
394PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
3104PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674

NCS ensembles :
ID
1
2
3
4

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Components

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Potassium-transporting ATPase ... , 4 types, 12 molecules AEIBFJCGKDHL

#1: Protein Potassium-transporting ATPase potassium-binding subunit / ATP phosphohydrolase [potassium-transporting] A chain / Potassium-binding and translocating subunit ...ATP phosphohydrolase [potassium-transporting] A chain / Potassium-binding and translocating subunit A / Potassium-translocating ATPase A chain


Mass: 59247.684 Da / Num. of mol.: 3 / Mutation: Q116R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdpA, b0698, JW0686 / Production host: Escherichia coli (E. coli) / Variant (production host): TK2498 / References: UniProt: P03959
#2: Protein Potassium-transporting ATPase ATP-binding subunit / ATP phosphohydrolase [potassium-transporting] B chain / Potassium-binding and translocating subunit ...ATP phosphohydrolase [potassium-transporting] B chain / Potassium-binding and translocating subunit B / Potassium-translocating ATPase B chain


Mass: 71417.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdpB, b0697, JW0685 / Production host: Escherichia coli (E. coli) / Variant (production host): TK2498 / References: UniProt: P03960, EC: 3.6.3.12
#3: Protein Potassium-transporting ATPase KdpC subunit / ATP phosphohydrolase [potassium-transporting] C chain / Potassium-binding and translocating subunit ...ATP phosphohydrolase [potassium-transporting] C chain / Potassium-binding and translocating subunit C / Potassium-translocating ATPase C chain


Mass: 20005.709 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdpC, JD73_10370 / Production host: Escherichia coli (E. coli) / Variant (production host): TK2498 / References: UniProt: A0A085P4P2, UniProt: P03961*PLUS
#4: Protein/peptide Potassium-transporting ATPase KdpF subunit / ATP phosphohydrolase [potassium-transporting] F chain / Potassium-binding and translocating subunit ...ATP phosphohydrolase [potassium-transporting] F chain / Potassium-binding and translocating subunit F / Potassium-translocating ATPase F chain


Mass: 2853.463 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdpF, b4513, JW0687 / Production host: Escherichia coli (E. coli) / Variant (production host): TK2498 / References: UniProt: P36937

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Sugars , 1 types, 4 molecules

#7: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 12 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.22 Å3/Da / Density % sol: 70.83 %
Description: Crystals appeared within a week and grew to full size (100 x 300 x 40 um) after three weeks.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% (w/v) PEG3350, 0.5-1.0 M NaCl, 0.05 mM sodium citrate pH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03666 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03666 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 167947 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 18.8 % / Biso Wilson estimate: 94.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.201 / Net I/σ(I): 11.28
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.9-318.54.910.960.488198.9
3-3.519.3452.5911.950.865199.2
3.5-418.850.7075.920.986199.3
4-518.5370.19315.90.998199.5
5-619.2240.12823.210.998199.7
6-717.7520.09828.690.998199.8
7-817.5920.06738.710.999199.7
8-918.3780.05346.40.999199.8
9-1217.7450.04350.030.999199.8
12-1516.0070.04247.761199.7
15-19.97418.1350.03752.30.999196.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.9→20 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.8
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 8341 5 %Random
Rwork0.243 ---
obs0.2446 166954 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 488.57 Å2 / Biso mean: 151.7128 Å2 / Biso min: 61.96 Å2
Refinement stepCycle: final / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32334 0 329 3 32666
Biso mean--195.59 109.22 -
Num. residues----4335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00233254
X-RAY DIFFRACTIONf_angle_d0.44845199
X-RAY DIFFRACTIONf_chiral_restr0.0375432
X-RAY DIFFRACTIONf_plane_restr0.0035700
X-RAY DIFFRACTIONf_dihedral_angle_d8.77619780
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D342X-RAY DIFFRACTION4.608TORSIONAL
12H342X-RAY DIFFRACTION4.608TORSIONAL
13L342X-RAY DIFFRACTION4.608TORSIONAL
21A7559X-RAY DIFFRACTION4.608TORSIONAL
22E7559X-RAY DIFFRACTION4.608TORSIONAL
23I7559X-RAY DIFFRACTION4.608TORSIONAL
31G2611X-RAY DIFFRACTION4.608TORSIONAL
32C2611X-RAY DIFFRACTION4.608TORSIONAL
33K2611X-RAY DIFFRACTION4.608TORSIONAL
41F9259X-RAY DIFFRACTION4.608TORSIONAL
42B9259X-RAY DIFFRACTION4.608TORSIONAL
43J9259X-RAY DIFFRACTION4.608TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.93290.54162770.56225248552599
2.9329-2.96730.60172790.54225305558499
2.9673-3.00330.54152730.51445187546099
3.0033-3.04120.53912780.50865276555499
3.0412-3.08110.49912740.48495240551499
3.0811-3.12310.47632780.44815284556299
3.1231-3.16760.45132730.42495213548699
3.1676-3.21470.45432770.40445256553399
3.2147-3.26470.41932730.38585255552899
3.2647-3.3180.38772780.3575257553599
3.318-3.37490.37682770.34345291556899
3.3749-3.4360.38442760.32365230550699
3.436-3.50170.34632790.31375297557699
3.5017-3.57280.35792780.29715269554799
3.5728-3.65010.31462750.27925264553999
3.6501-3.73440.3142750.26815221549699
3.7344-3.82720.26092740.25165277555199
3.8272-3.92990.29642770.2415262553998
3.9299-4.04460.27392790.23525299557899
4.0446-4.1740.25612800.21815314559499
4.174-4.32180.24832790.21185282556199
4.3218-4.49290.24842790.21535305558499
4.4929-4.69490.27022790.19295282556199
4.6949-4.93890.22322810.184953295610100
4.9389-5.2430.21922800.193753275607100
5.243-5.63940.22852800.200753195599100
5.6394-6.19150.26362830.224753595642100
6.1915-7.05270.26292820.216253585640100
7.0527-8.75910.21452830.181553765659100
8.7591-19.97410.20182850.194354315716100
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)
10.926-0.27560.55030.34-0.15080.73420.2230.156-0.0643-0.13430.0790.15720.25790.183300.87740.09570.0240.8138-0.09510.8663141.2138-34.3355-21.4678
20.1285-0.19780.35820.2159-0.26560.44640.1499-0.1688-0.07210.2314-0.0484-0.06970.16890.194601.02490.13220.00061.4137-0.15651.1228169.2423-29.2323-1.0695
30.1416-0.087-0.15370.13910.10410.15840.1991-0.0576-0.4255-0.0140.12410.74990.1516-0.232801.36380.05450.04561.36610.07961.781866.3133-34.7871-30.9703
40.22850.08010.22990.18240.09670.1388-0.13030.37930.036-0.52780.12440.01760.0155-0.087501.56570.2479-0.16141.21340.12071.650767.1057-5.6108-35.6346
50.7332-0.547-0.18980.3361-0.0320.40160.10370.5409-0.211-0.27990.01710.0992-0.22360.077201.271-0.0125-0.17141.23790.02631.300193.1447-15.6712-35.3119
60.70570.49940.02160.78870.58751.67130.2743-0.7893-0.1107-0.2099-0.03270.26520.3035-0.27810.00240.7007-0.16-0.01951.24750.20671.0693106.7075-32.5601-2.995
70.51330.53520.02770.66720.02230.96980.0356-0.022-0.0127-0.02570.1068-00.0087-0.455600.58150.22030.08730.9168-0.06790.7705157.6559-23.476843.0288
80.0808-0.16070.0646-0.0152-0.10620.04390.08520.0926-0.03450.30670.2027-0.09860.0862-0.197101.52590.0136-0.08681.39450.04741.2626162.4143-43.072871.7055
90.09360.0585-0.07790.1947-0.27290.27560.1123-0.26640.1537-0.35480.3640.8152-0.2555-0.4704-01.4872-0.2863-0.13961.7282-0.14821.863180.646735.3461-0.1248
100.0525-0.11740.14290.1849-0.1920.1751-0.2804-0.33560.0838-1.11550.4651-0.67770.0380.24830.00011.814-0.28590.2411.9082-0.221.4806202.623918.045-10.136
110.4594-0.0944-0.30940.3820.11540.1832-0.0190.4827-0.1205-0.4060.36710.0362-0.10840.002601.4199-0.031-0.02761.5961-0.19831.2551183.60772.31013.7647
121.3873-0.0096-0.03910.44440.07250.81860.1065-0.02460.11590.42270.0231-0.2233-0.71120.300101.32650.01540.01980.7168-0.0580.9462179.29869.051541.5556
130.0329-0.05340.19180.61430.38760.78660.00530.2173-0.0897-0.22740.0330.0703-0.23090.32601.0648-0.0458-0.02460.93570.0030.8771125.5608-23.2319-86.0464
14-0.02120.12990.1680.11630.03190.1186-0.1382-0.38690.05720.24150.1291-0.2787-0.20150.139801.4478-0.0426-0.06921.102-0.09471.1569121.3135-8.9862-54.3416
150.09130.0684-0.17890.1828-0.11090.2487-0.0591-0.1979-0.23570.0460.1149-1.39270.57511.7192-0.01171.87670.0984-0.04271.9011-0.46962.158148.996-81.9195-128.4143
160.03570.0205-0.1004-0.0037-0.07010.16320.22080.6514-0.11940.03580.2066-0.3578-0.0805-0.108301.85990.2289-0.51171.3395-0.29241.7772122.6725-94.634-123.9122
170.19320.07750.13290.1989-0.05390.1407-0.06410.1534-0.1852-0.06960.25690.3726-0.1552-0.082701.85910.201-0.35641.4828-0.20731.5367121.112-68.0019-114.8072
181.69060.3329-0.29220.974-0.47731.10930.07920.0715-0.24910.16390.3059-0.14650.64150.768601.22150.4415-0.1951.4511-0.35991.172145.0579-57.0859-86.5522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not resseq 199:217 and not resseq 305:328 or chain C and not resseq 40:190 or chain M and resseq 1301:1302 or chain N and resid 2A1 - 199
2X-RAY DIFFRACTION1chain A and not resseq 199:217 and not resseq 305:328 or chain C and not resseq 40:190 or chain M and resseq 1301:1302 or chain N and resid 2A199 - 217
3X-RAY DIFFRACTION1chain A and not resseq 199:217 and not resseq 305:328 or chain C and not resseq 40:190 or chain M and resseq 1301:1302 or chain N and resid 2A217 - 557
4X-RAY DIFFRACTION2chain A and resseq 199:217 or chain A and resseq 305:328 or chain C and resseq 40:190A0
5X-RAY DIFFRACTION3chain B and resseq 103:196B103 - 196
6X-RAY DIFFRACTION4chain B and resseq 318:447B318 - 447
7X-RAY DIFFRACTION5chain B and resseq 287:554 and not resseq 318:447B9 - 318
8X-RAY DIFFRACTION5chain B and resseq 287:554 and not resseq 318:447B447 - 682
9X-RAY DIFFRACTION6chain B and not resseq 103:196 and not resseq 287:554 or chain D or chain N and resid 1B9 - 103
10X-RAY DIFFRACTION6chain B and not resseq 103:196 and not resseq 287:554 or chain D or chain N and resid 1B196 - 682
11X-RAY DIFFRACTION7chain E and not resseq 199:217 and not resseq 305:328 or chain G and not resseq 40:190 or chain M and resseq 1303:1304 or chain N and resid 3E1 - 199
12X-RAY DIFFRACTION7chain E and not resseq 199:217 and not resseq 305:328 or chain G and not resseq 40:190 or chain M and resseq 1303:1304 or chain N and resid 3E199 - 217
13X-RAY DIFFRACTION7chain E and not resseq 199:217 and not resseq 305:328 or chain G and not resseq 40:190 or chain M and resseq 1303:1304 or chain N and resid 3E217 - 557
14X-RAY DIFFRACTION8chain E and resseq 199:217 or chain E and resseq 305:328 or chain G and resseq 40:190E0
15X-RAY DIFFRACTION9chain F and resseq 103:196F103 - 196
16X-RAY DIFFRACTION10chain F and resseq 318:447F318 - 447
17X-RAY DIFFRACTION11chain F and resseq 287:554 and not resseq 318:447F9 - 318
18X-RAY DIFFRACTION11chain F and resseq 287:554 and not resseq 318:447F447 - 682
19X-RAY DIFFRACTION12chain F and not resseq 103:196 and not resseq 287:554 or chain HF9 - 103
20X-RAY DIFFRACTION12chain F and not resseq 103:196 and not resseq 287:554 or chain HF103 - 196
21X-RAY DIFFRACTION12chain F and not resseq 103:196 and not resseq 287:554 or chain HF196 - 682
22X-RAY DIFFRACTION13chain I and not resseq 199:217 and not resseq 305:328 or chain K and not resseq 40:190 or chain M and resseq 1305:1306 or chain N and resid 4I1 - 199
23X-RAY DIFFRACTION13chain I and not resseq 199:217 and not resseq 305:328 or chain K and not resseq 40:190 or chain M and resseq 1305:1306 or chain N and resid 4I199 - 217
24X-RAY DIFFRACTION13chain I and not resseq 199:217 and not resseq 305:328 or chain K and not resseq 40:190 or chain M and resseq 1305:1306 or chain N and resid 4I217 - 557
25X-RAY DIFFRACTION14chain I and resseq 199:217 or chain I and resseq 305:328 or chain K and resseq 40:190I0
26X-RAY DIFFRACTION15chain J and resseq 103:196J103 - 196
27X-RAY DIFFRACTION16chain J and resseq 318:447J318 - 447
28X-RAY DIFFRACTION17chain J and resseq 287:554 and not resseq 318:447J9 - 318
29X-RAY DIFFRACTION17chain J and resseq 287:554 and not resseq 318:447J447 - 682
30X-RAY DIFFRACTION18chain J and not resseq 103:196 and not resseq 287:554 or chain LJ9 - 103
31X-RAY DIFFRACTION18chain J and not resseq 103:196 and not resseq 287:554 or chain LJ103 - 196
32X-RAY DIFFRACTION18chain J and not resseq 103:196 and not resseq 287:554 or chain LJ196 - 682

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