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- PDB-4ucq: Structure of the T18D small subunit mutant of D. fructosovorans N... -

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Basic information

Entry
Database: PDB / ID: 4ucq
TitleStructure of the T18D small subunit mutant of D. fructosovorans NiFe- hydrogenase
Components
  • HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
  • NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / CARBONMONOXIDE-(DICYANO) IRON / NICKEL (II) ION / IRON/SULFUR CLUSTER / Nickel-dependent hydrogenase large subunit / cytochrome-c3 hydrogenase / Periplasmic [NiFe] hydrogenase small subunit / Periplasmic [NiFe] hydrogenase large subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO FRUCTOSIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAbou-Hamdan, A. / Ceccaldi, P. / Lebrette, H. / Guttierez-Sanz, O. / Richaud, P. / Cournac, L. / Guigliarelli, B. / deLacey, A.L. / Leger, C. / Volbeda, A. ...Abou-Hamdan, A. / Ceccaldi, P. / Lebrette, H. / Guttierez-Sanz, O. / Richaud, P. / Cournac, L. / Guigliarelli, B. / deLacey, A.L. / Leger, C. / Volbeda, A. / Burlat, B. / Dementin, S.
CitationJournal: J. Biol. Chem. / Year: 2015
Title: A threonine stabilizes the NiC and NiR catalytic intermediates of [NiFe]-hydrogenase.
Authors: Abou-Hamdan, A. / Ceccaldi, P. / Lebrette, H. / Gutierrez-Sanz, O. / Richaud, P. / Cournac, L. / Guigliarelli, B. / De Lacey, A.L. / Leger, C. / Volbeda, A. / Burlat, B. / Dementin, S.
History
DepositionDec 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / citation_author / exptl_crystal_grow
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.3Dec 20, 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_conn_type / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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 / _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: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,89330
Polymers268,6866
Non-polymers4,20624
Water8,035446
1
A: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
Q: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,05611
Polymers89,5622
Non-polymers1,4949
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-124.1 kcal/mol
Surface area25300 Å2
MethodPISA
2
B: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
R: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,96410
Polymers89,5622
Non-polymers1,4028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-123.4 kcal/mol
Surface area25170 Å2
MethodPISA
3
C: HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
S: NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8729
Polymers89,5622
Non-polymers1,3107
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-122.2 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.800, 99.900, 183.300
Angle α, β, γ (deg.)90.00, 91.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14Q
24R
34S
15Q
25R
35S
16Q
26R
36S

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERILEILEAA8 - 288 - 28
211SERSERILEILEBB8 - 288 - 28
311SERSERILEILECC8 - 288 - 28
121TYRTYRILEILEAA31 - 3631 - 36
221TYRTYRILEILEBB31 - 3631 - 36
321TYRTYRILEILECC31 - 3631 - 36
131ILEILEGLYGLYAA40 - 5340 - 53
231ILEILEGLYGLYBB40 - 5340 - 53
331ILEILEGLYGLYCC40 - 5340 - 53
141ALAALAGLUGLUAA56 - 5756 - 57
241ALAALAGLUGLUBB56 - 5756 - 57
341ALAALAGLUGLUCC56 - 5756 - 57
151ALAALALEULEUAA59 - 6059 - 60
251ALAALALEULEUBB59 - 6059 - 60
351ALAALALEULEUCC59 - 6059 - 60
161ALAALALEULEUAA63 - 6463 - 64
261ALAALALEULEUBB63 - 6463 - 64
361ALAALALEULEUCC63 - 6463 - 64
171GLYGLYTYRTYRAA69 - 7069 - 70
271GLYGLYTYRTYRBB69 - 7069 - 70
371GLYGLYTYRTYRCC69 - 7069 - 70
181LEULEUILEILEAA72 - 8172 - 81
281LEULEUILEILEBB72 - 8172 - 81
381LEULEUILEILECC72 - 8172 - 81
191TRPTRPGLYGLYAA86 - 9186 - 91
291TRPTRPGLYGLYBB86 - 9186 - 91
391TRPTRPGLYGLYCC86 - 9186 - 91
1101PROPROMETMETAA93 - 9493 - 94
2101PROPROMETMETBB93 - 9493 - 94
3101PROPROMETMETCC93 - 9493 - 94
112GLYGLYPROPROAA173 - 175173 - 175
212GLYGLYPROPROBB173 - 175173 - 175
312GLYGLYPROPROCC173 - 175173 - 175
122PHEPHETYRTYRAA178 - 179178 - 179
222PHEPHETYRTYRBB178 - 179178 - 179
322PHEPHETYRTYRCC178 - 179178 - 179
132VALVALCYSCYSAA183 - 187183 - 187
232VALVALCYSCYSBB183 - 187183 - 187
332VALVALCYSCYSCC183 - 187183 - 187
142ALAALAPHEPHEAA199 - 202199 - 202
242ALAALAPHEPHEBB199 - 202199 - 202
342ALAALAPHEPHECC199 - 202199 - 202
152SERSERSERSERAA204204
252SERSERSERSERBB204204
352SERSERSERSERCC204204
162ALAALALYSLYSAA207 - 208207 - 208
262ALAALALYSLYSBB207 - 208207 - 208
362ALAALALYSLYSCC207 - 208207 - 208
172GLYGLYLEULEUAA210 - 213210 - 213
272GLYGLYLEULEUBB210 - 213210 - 213
372GLYGLYLEULEUCC210 - 213210 - 213
182LEULEUGLYGLYAA216 - 220216 - 220
282LEULEUGLYGLYBB216 - 220216 - 220
382LEULEUGLYGLYCC216 - 220216 - 220
192VALVALPROPROAA222 - 228222 - 228
292VALVALPROPROBB222 - 228222 - 228
392VALVALPROPROCC222 - 228222 - 228
1102VALVALASNASNAA230 - 233230 - 233
2102VALVALASNASNBB230 - 233230 - 233
3102VALVALASNASNCC230 - 233230 - 233
113VALVALTRPTRPAA235 - 254235 - 254
213VALVALTRPTRPBB235 - 254235 - 254
313VALVALTRPTRPCC235 - 254235 - 254
123THRTHRTHRTHRAA256 - 258256 - 258
223THRTHRTHRTHRBB256 - 258256 - 258
323THRTHRTHRTHRCC256 - 258256 - 258
133PHEPHETYRTYRAA260 - 261260 - 261
233PHEPHETYRTYRBB260 - 261260 - 261
333PHEPHETYRTYRCC260 - 261260 - 261
143SF4SF4F3SF3SAG - H1265 - 1266
243SF4SF4F3SF3SBK - L1265 - 1266
343SF4SF4F3SF3SCN - O1265 - 1266
114PROPROVALVALQD15 - 3229 - 46
214PROPROVALVALRE15 - 3229 - 46
314PROPROVALVALSF15 - 3229 - 46
124ASPASPLEULEUQD41 - 5655 - 70
224ASPASPLEULEURE41 - 5655 - 70
324ASPASPLEULEUSF41 - 5655 - 70
134GLYGLYPROPROQD58 - 6172 - 75
234GLYGLYPROPRORE58 - 6172 - 75
334GLYGLYPROPROSF58 - 6172 - 75
144GLYGLYVALVALQD58 - 9172 - 105
244GLYGLYVALVALRE58 - 9172 - 105
344GLYGLYVALVALSF58 - 9172 - 105
154ILEILEHISHISQD95 - 115109 - 129
254ILEILEHISHISRE95 - 115109 - 129
354ILEILEHISHISSF95 - 115109 - 129
164VALVALVALVALQD117 - 130131 - 144
264VALVALVALVALRE117 - 130131 - 144
364VALVALVALVALSF117 - 130131 - 144
174GLYGLYTHRTHRQD177 - 180191 - 194
274GLYGLYTHRTHRRE177 - 180191 - 194
374GLYGLYTHRTHRSF177 - 180191 - 194
184VALVALTYRTYRQD197 - 205211 - 219
284VALVALTYRTYRRE197 - 205211 - 219
384VALVALTYRTYRSF197 - 205211 - 219
194ALAALATYRTYRQD215 - 240229 - 254
294ALAALATYRTYRRE215 - 240229 - 254
394ALAALATYRTYRSF215 - 240229 - 254
1104GLYGLYMETMETQD423 - 439437 - 453
2104GLYGLYMETMETRE423 - 439437 - 453
3104GLYGLYMETMETSF423 - 439437 - 453
115GLYGLYILEILEQD468 - 483482 - 497
215GLYGLYILEILERE468 - 483482 - 497
315GLYGLYILEILESF468 - 483482 - 497
125PHEPHEPROPROQD493 - 505507 - 519
225PHEPHEPROPRORE493 - 505507 - 519
325PHEPHEPROPROSF493 - 505507 - 519
135GLYGLYALAALAQD521 - 525535 - 539
235GLYGLYALAALARE521 - 525535 - 539
335GLYGLYALAALASF521 - 525535 - 539
145PROPROILEILEQD530 - 533544 - 547
245PROPROILEILERE530 - 533544 - 547
345PROPROILEILESF530 - 533544 - 547
155LEULEUHISHISQD534 - 549548 - 563
255LEULEUHISHISRE534 - 549548 - 563
355LEULEUHISHISSF534 - 549548 - 563
165FCOFCOMGMGQQ - S1550 - 1553
265FCOFCOMGMGRV - X1550 - 1553
365FCOFCOMGMGSAA - CA1550 - 1553
116TRPTRPTHRTHRQD280 - 286294 - 300
216TRPTRPTHRTHRRE280 - 286294 - 300
316TRPTRPTHRTHRSF280 - 286294 - 300
126TYRTYRASPASPQD289 - 299303 - 313
226TYRTYRASPASPRE289 - 299303 - 313
326TYRTYRASPASPSF289 - 299303 - 313
136SERSERPROPROQD301 - 302315 - 316
236SERSERPROPRORE301 - 302315 - 316
336SERSERPROPROSF301 - 302315 - 316
146LYSLYSGLYGLYQD304 - 318318 - 332
246LYSLYSGLYGLYRE304 - 318318 - 332
346LYSLYSGLYGLYSF304 - 318318 - 332
156TYRTYRTYRTYRQD368 - 376382 - 390
256TYRTYRTYRTYRRE368 - 376382 - 390
356TYRTYRTYRTYRSF368 - 376382 - 390
166ALAALAALAALAQD380 - 392394 - 406
266ALAALAALAALARE380 - 392394 - 406
366ALAALAALAALASF380 - 392394 - 406

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.365036, -0.741312, -0.56321), (0.733363, -0.601634, 0.316568), (-0.573522, -0.297479, 0.763269)0.509, 3.342, 69.033
2given(0.384375, -0.739964, 0.552004), (-0.747114, -0.600573, -0.284837), (0.542288, -0.302926, -0.783683)-35.745, -27.714, 54.357
3given(-0.35624, -0.744661, -0.564422), (0.736872, -0.595317, 0.320338), (-0.574554, -0.30179, 0.760796)0.38, 3.351, 69.021
4given(0.390809, -0.73215, 0.557875), (-0.742085, -0.609189, -0.279639), (0.544589, -0.304706, -0.781394)-35.936, -27.743, 54.383
5given(1), (1), (1)
6given(-0.362027, 0.731772, -0.577448), (-0.74076, -0.601891, -0.298333), (-0.565872, 0.319746, 0.759968)37.69749, 23.00899, -53.25977
7given(0.38167, -0.744905, 0.547215), (-0.739897, -0.601056, -0.302134), (0.553968, -0.289567, -0.780558)-36.66267, -26.69561, 54.20607
8given(1), (1), (1)
9given(-0.367446, 0.736183, -0.568347), (-0.743244, -0.599786, -0.296386), (-0.559081, 0.313515, 0.767553)36.96033, 22.81609, -53.64858
10given(0.390314, -0.747271, 0.537811), (-0.736622, -0.603887, -0.304481), (0.552307, -0.277321, -0.786162)-35.95855, -26.55375, 54.92398
11given(1), (1), (1)
12given(-0.363979, 0.734935, -0.572179), (-0.744702, -0.598593, -0.295136), (-0.559408, 0.31868, 0.765183)37.25957, 22.75828, -53.53877
13given(0.385351, -0.746943, 0.54183), (-0.735505, -0.60322, -0.308479), (0.557259, -0.279646, -0.781832)-36.39349, -26.20334, 54.75871
14given(1), (1), (1)
15given(-0.355834, 0.738372, -0.572877), (-0.74678, -0.593202, -0.300718), (-0.561874, 0.320808, 0.762483)37.17603, 22.98061, -53.4872
16given(0.391132, -0.7417, 0.544883), (-0.729933, -0.610601, -0.307189), (0.560548, -0.277576, -0.780216)-36.16404, -26.49448, 54.86152
17given(1), (1), (1)
18given(-0.354642, 0.738435, -0.573535), (-0.743884, -0.594452, -0.30539), (-0.56645, 0.31834, 0.760128)37.2289, 23.37354, -53.27959
19given(0.393958, -0.738078, 0.547758), (-0.731063, -0.612833, -0.299969), (0.557085, -0.282271, -0.781012)-36.10778, -26.97938, 54.69287
20given(1), (1), (1)
21given(-0.355429, 0.736725, -0.575245), (-0.744123, -0.595458, -0.302838), (-0.565642, 0.320416, 0.759857)37.41205, 23.18899, -53.28474
22given(0.386275, -0.74492, 0.543954), (-0.736144, -0.604303, -0.304812), (0.555773, -0.282687, -0.781795)-36.25875, -26.56927, 54.72903

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Components

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Protein , 2 types, 6 molecules ABCQRS

#1: Protein HYDROGENASE (NIFE) SMALL SUBUNIT HYDA / NIFE-HYDROGENASE SMALL SUBUNIT


Mass: 28361.299 Da / Num. of mol.: 3 / Fragment: RESIDUES 51-314 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSIVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
References: UniProt: E1K248, UniProt: P18187*PLUS, cytochrome-c3 hydrogenase
#2: Protein NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT / / NIFE-HYDROGENASE LARGE SUBUNIT


Mass: 61200.785 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO FRUCTOSIVORANS (bacteria)
Production host: DESULFOVIBRIO FRUCTOSIVORANS JJ (bacteria)
References: UniProt: E1K247, UniProt: P18188*PLUS, cytochrome-c3 hydrogenase

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Non-polymers , 7 types, 470 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3FeN2O
#7: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL STREP TAG

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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: 43.46 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: VAPOR DIFFUSION, PH 6.3, 293K; PEG6000, MES, UNDER AIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 70368 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.4 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQW

1yqw


Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.909 / SU B: 33.494 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24133 3462 4.9 %RANDOM
Rwork0.19777 ---
obs0.1999 66841 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.085 Å2
Baniso -1Baniso -2Baniso -3
1-3.81 Å20 Å22.12 Å2
2--0.18 Å20 Å2
3----4.12 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18408 0 132 446 18986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01919142
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.97725928
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31152410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38524.417772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.609153043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4521573
X-RAY DIFFRACTIONr_chiral_restr0.1010.22838
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6850.4839658
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0590.72112062
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8150.59484
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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 / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A4911.01
12B4911.28
13C4911.51
21A2821.06
22B2821.34
23C2821.32
31A2020.78
32B2021.23
33C2021.24
41Q12461.12
42R12461.09
43S12461.43
51Q4001.21
52R4001.12
53S4001.27
61Q4331.74
62R4331.81
63S4332.05
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 264 -
Rwork0.296 4779 -
obs--96.52 %
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)
11.2227-0.3162-0.53640.85740.22641.9134-0.00420.09680.1464-0.12290.0219-0.1612-0.11610.0603-0.01780.6631-0.00190.11190.02330.02280.381912.319714.25135.1977
21.0039-0.0748-0.24491.07480.46751.568-0.1185-0.0072-0.12790.11790.0442-0.04820.4970.01020.07430.84490.02390.15650.00380.02060.3397.9842-7.143314.8819
31.18050.2316-1.07981.3257-0.34463.8082-0.23990.1294-0.1766-0.2912-0.01470.12440.9487-0.72290.25450.4571-0.1469-0.00160.3039-0.07820.3632-17.38895.477861.7689
41.81970.3397-1.45271.3202-0.44983.68910.1192-0.49390.03940.1459-0.1949-0.0562-0.08520.42720.07570.212-0.0425-0.04130.3012-0.00440.3461-5.568218.282577.9724
52.3408-0.12030.84411.08360.40031.326-0.15310.0715-0.27440.1162-0.06370.37040.5598-0.53010.21680.8388-0.11430.18040.53720.00520.6178-38.7261-46.750952.8251
61.4558-0.2284-1.17791.26650.0843.8628-0.0313-0.20210.01560.01490.0525-0.0238-0.1970.3831-0.02110.47980.03230.01580.36250.0210.4179-19.1617-33.564949.339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 264
2X-RAY DIFFRACTION1A1265 - 1267
3X-RAY DIFFRACTION1A1271
4X-RAY DIFFRACTION1A2001 - 2047
5X-RAY DIFFRACTION2Q6 - 549
6X-RAY DIFFRACTION2Q1550 - 1553
7X-RAY DIFFRACTION2Q1561 - 1562
8X-RAY DIFFRACTION2Q2001 - 2116
9X-RAY DIFFRACTION3B3 - 264
10X-RAY DIFFRACTION3B1265 - 1267
11X-RAY DIFFRACTION3B2001 - 2044
12X-RAY DIFFRACTION4R5 - 549
13X-RAY DIFFRACTION4R1550 - 1553
14X-RAY DIFFRACTION4R1563
15X-RAY DIFFRACTION4R2001 - 2106
16X-RAY DIFFRACTION5C5 - 264
17X-RAY DIFFRACTION5C1265 - 1268
18X-RAY DIFFRACTION5C2001 - 2046
19X-RAY DIFFRACTION6S6 - 549
20X-RAY DIFFRACTION6S1550 - 1553
21X-RAY DIFFRACTION6S1561
22X-RAY DIFFRACTION6S2001 - 2073

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