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- PDB-5tig: CRYSTAL STRUCTURE OF 4-OXALOCROTONATE TAUTOMERASE INACTIVATED BY BrHPD -

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Basic information

Entry
Database: PDB / ID: 5tig
TitleCRYSTAL STRUCTURE OF 4-OXALOCROTONATE TAUTOMERASE INACTIVATED BY BrHPD
Components2-hydroxymuconate tautomerase
KeywordsISOMERASE/ISOMERASE INHIBITOR / ISOMERASE / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


xylene catabolic process / 2-hydroxymuconate tautomerase / toluene catabolic process / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(3E)-5-hydroxy-2-oxopent-3-enoic acid / 2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhang, Y. / Li, W. / Stack, T.
CitationJournal: Biochemistry / Year: 2018
Title: Inactivation of 4-Oxalocrotonate Tautomerase by 5-Halo-2-hydroxy-2,4-pentadienoates.
Authors: Stack, T.M.M. / Li, W. / Johnson, W.H. / Zhang, Y.J. / Whitman, C.P.
History
DepositionOct 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 17, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 2-hydroxymuconate tautomerase
B: 2-hydroxymuconate tautomerase
C: 2-hydroxymuconate tautomerase
D: 2-hydroxymuconate tautomerase
E: 2-hydroxymuconate tautomerase
F: 2-hydroxymuconate tautomerase
G: 2-hydroxymuconate tautomerase
H: 2-hydroxymuconate tautomerase
I: 2-hydroxymuconate tautomerase
J: 2-hydroxymuconate tautomerase
K: 2-hydroxymuconate tautomerase
L: 2-hydroxymuconate tautomerase
M: 2-hydroxymuconate tautomerase
N: 2-hydroxymuconate tautomerase
O: 2-hydroxymuconate tautomerase
P: 2-hydroxymuconate tautomerase
Q: 2-hydroxymuconate tautomerase
R: 2-hydroxymuconate tautomerase
S: 2-hydroxymuconate tautomerase
T: 2-hydroxymuconate tautomerase
U: 2-hydroxymuconate tautomerase
V: 2-hydroxymuconate tautomerase
W: 2-hydroxymuconate tautomerase
X: 2-hydroxymuconate tautomerase
Y: 2-hydroxymuconate tautomerase
Z: 2-hydroxymuconate tautomerase
a: 2-hydroxymuconate tautomerase
b: 2-hydroxymuconate tautomerase
c: 2-hydroxymuconate tautomerase
d: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,82639
Polymers204,65530
Non-polymers1,1719
Water2,180121
1
A: 2-hydroxymuconate tautomerase
B: 2-hydroxymuconate tautomerase
C: 2-hydroxymuconate tautomerase
D: 2-hydroxymuconate tautomerase
E: 2-hydroxymuconate tautomerase
F: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,45110
Polymers40,9316
Non-polymers5204
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13180 Å2
ΔGint-71 kcal/mol
Surface area14500 Å2
MethodPISA
2
G: 2-hydroxymuconate tautomerase
H: 2-hydroxymuconate tautomerase
I: 2-hydroxymuconate tautomerase
J: 2-hydroxymuconate tautomerase
K: 2-hydroxymuconate tautomerase
L: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1918
Polymers40,9316
Non-polymers2602
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint-71 kcal/mol
Surface area14510 Å2
MethodPISA
3
M: 2-hydroxymuconate tautomerase
N: 2-hydroxymuconate tautomerase
O: 2-hydroxymuconate tautomerase
P: 2-hydroxymuconate tautomerase
Q: 2-hydroxymuconate tautomerase
R: 2-hydroxymuconate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3219
Polymers40,9316
Non-polymers3903
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13080 Å2
ΔGint-67 kcal/mol
Surface area14130 Å2
MethodPISA
4
S: 2-hydroxymuconate tautomerase
T: 2-hydroxymuconate tautomerase
U: 2-hydroxymuconate tautomerase
V: 2-hydroxymuconate tautomerase
W: 2-hydroxymuconate tautomerase
X: 2-hydroxymuconate tautomerase


Theoretical massNumber of molelcules
Total (without water)40,9316
Polymers40,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-68 kcal/mol
Surface area14230 Å2
MethodPISA
5
Y: 2-hydroxymuconate tautomerase
Z: 2-hydroxymuconate tautomerase
a: 2-hydroxymuconate tautomerase
b: 2-hydroxymuconate tautomerase
c: 2-hydroxymuconate tautomerase
d: 2-hydroxymuconate tautomerase


Theoretical massNumber of molelcules
Total (without water)40,9316
Polymers40,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-70 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.746, 90.121, 171.445
Angle α, β, γ (deg.)90.000, 96.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114A
214O
115A
215P
116A
216Q
117A
217R
118A
218S
119A
219T
120A
220U
121A
221V
122A
222W
123A
223X
124A
224Y
125A
225Z
126A
226a
127A
227b
128A
228c
129A
229d
130B
230C
131B
231D
132B
232E
133B
233F
134B
234G
135B
235H
136B
236I
137B
237J
138B
238K
139B
239L
140B
240M
141B
241N
142B
242O
143B
243P
144B
244Q
145B
245R
146B
246S
147B
247T
148B
248U
149B
249V
150B
250W
151B
251X
152B
252Y
153B
253Z
154B
254a
155B
255b
156B
256c
157B
257d
158C
258D
159C
259E
160C
260F
161C
261G
162C
262H
163C
263I
164C
264J
165C
265K
166C
266L
167C
267M
168C
268N
169C
269O
170C
270P
171C
271Q
172C
272R
173C
273S
174C
274T
175C
275U
176C
276V
177C
277W
178C
278X
179C
279Y
180C
280Z
181C
281a
182C
282b
183C
283c
184C
284d
185D
285E
186D
286F
187D
287G
188D
288H
189D
289I
190D
290J
191D
291K
192D
292L
193D
293M
194D
294N
195D
295O
196D
296P
197D
297Q
198D
298R
199D
299S
1100D
2100T
1101D
2101U
1102D
2102V
1103D
2103W
1104D
2104X
1105D
2105Y
1106D
2106Z
1107D
2107a
1108D
2108b
1109D
2109c
1110D
2110d
1111E
2111F
1112E
2112G
1113E
2113H
1114E
2114I
1115E
2115J
1116E
2116K
1117E
2117L
1118E
2118M
1119E
2119N
1120E
2120O
1121E
2121P
1122E
2122Q
1123E
2123R
1124E
2124S
1125E
2125T
1126E
2126U
1127E
2127V
1128E
2128W
1129E
2129X
1130E
2130Y
1131E
2131Z
1132E
2132a
1133E
2133b
1134E
2134c
1135E
2135d
1136F
2136G
1137F
2137H
1138F
2138I
1139F
2139J
1140F
2140K
1141F
2141L
1142F
2142M
1143F
2143N
1144F
2144O
1145F
2145P
1146F
2146Q
1147F
2147R
1148F
2148S
1149F
2149T
1150F
2150U
1151F
2151V
1152F
2152W
1153F
2153X
1154F
2154Y
1155F
2155Z
1156F
2156a
1157F
2157b
1158F
2158c
1159F
2159d
1160G
2160H
1161G
2161I
1162G
2162J
1163G
2163K
1164G
2164L
1165G
2165M
1166G
2166N
1167G
2167O
1168G
2168P
1169G
2169Q
1170G
2170R
1171G
2171S
1172G
2172T
1173G
2173U
1174G
2174V
1175G
2175W
1176G
2176X
1177G
2177Y
1178G
2178Z
1179G
2179a
1180G
2180b
1181G
2181c
1182G
2182d
1183H
2183I
1184H
2184J
1185H
2185K
1186H
2186L
1187H
2187M
1188H
2188N
1189H
2189O
1190H
2190P
1191H
2191Q
1192H
2192R
1193H
2193S
1194H
2194T
1195H
2195U
1196H
2196V
1197H
2197W
1198H
2198X
1199H
2199Y
1200H
2200Z
1201H
2201a
1202H
2202b
1203H
2203c
1204H
2204d
1205I
2205J
1206I
2206K
1207I
2207L
1208I
2208M
1209I
2209N
1210I
2210O
1211I
2211P
1212I
2212Q
1213I
2213R
1214I
2214S
1215I
2215T
1216I
2216U
1217I
2217V
1218I
2218W
1219I
2219X
1220I
2220Y
1221I
2221Z
1222I
2222a
1223I
2223b
1224I
2224c
1225I
2225d
1226J
2226K
1227J
2227L
1228J
2228M
1229J
2229N
1230J
2230O
1231J
2231P
1232J
2232Q
1233J
2233R
1234J
2234S
1235J
2235T
1236J
2236U
1237J
2237V
1238J
2238W
1239J
2239X
1240J
2240Y
1241J
2241Z
1242J
2242a
1243J
2243b
1244J
2244c
1245J
2245d
1246K
2246L
1247K
2247M
1248K
2248N
1249K
2249O
1250K
2250P
1251K
2251Q
1252K
2252R
1253K
2253S
1254K
2254T
1255K
2255U
1256K
2256V
1257K
2257W
1258K
2258X
1259K
2259Y
1260K
2260Z
1261K
2261a
1262K
2262b
1263K
2263c
1264K
2264d
1265L
2265M
1266L
2266N
1267L
2267O
1268L
2268P
1269L
2269Q
1270L
2270R
1271L
2271S
1272L
2272T
1273L
2273U
1274L
2274V
1275L
2275W
1276L
2276X
1277L
2277Y
1278L
2278Z
1279L
2279a
1280L
2280b
1281L
2281c
1282L
2282d
1283M
2283N
1284M
2284O
1285M
2285P
1286M
2286Q
1287M
2287R
1288M
2288S
1289M
2289T
1290M
2290U
1291M
2291V
1292M
2292W
1293M
2293X
1294M
2294Y
1295M
2295Z
1296M
2296a
1297M
2297b
1298M
2298c
1299M
2299d
1300N
2300O
1301N
2301P
1302N
2302Q
1303N
2303R
1304N
2304S
1305N
2305T
1306N
2306U
1307N
2307V
1308N
2308W
1309N
2309X
1310N
2310Y
1311N
2311Z
1312N
2312a
1313N
2313b
1314N
2314c
1315N
2315d
1316O
2316P
1317O
2317Q
1318O
2318R
1319O
2319S
1320O
2320T
1321O
2321U
1322O
2322V
1323O
2323W
1324O
2324X
1325O
2325Y
1326O
2326Z
1327O
2327a
1328O
2328b
1329O
2329c
1330O
2330d
1331P
2331Q
1332P
2332R
1333P
2333S
1334P
2334T
1335P
2335U
1336P
2336V
1337P
2337W
1338P
2338X
1339P
2339Y
1340P
2340Z
1341P
2341a
1342P
2342b
1343P
2343c
1344P
2344d
1345Q
2345R
1346Q
2346S
1347Q
2347T
1348Q
2348U
1349Q
2349V
1350Q
2350W
1351Q
2351X
1352Q
2352Y
1353Q
2353Z
1354Q
2354a
1355Q
2355b
1356Q
2356c
1357Q
2357d
1358R
2358S
1359R
2359T
1360R
2360U
1361R
2361V
1362R
2362W
1363R
2363X
1364R
2364Y
1365R
2365Z
1366R
2366a
1367R
2367b
1368R
2368c
1369R
2369d
1370S
2370T
1371S
2371U
1372S
2372V
1373S
2373W
1374S
2374X
1375S
2375Y
1376S
2376Z
1377S
2377a
1378S
2378b
1379S
2379c
1380S
2380d
1381T
2381U
1382T
2382V
1383T
2383W
1384T
2384X
1385T
2385Y
1386T
2386Z
1387T
2387a
1388T
2388b
1389T
2389c
1390T
2390d
1391U
2391V
1392U
2392W
1393U
2393X
1394U
2394Y
1395U
2395Z
1396U
2396a
1397U
2397b
1398U
2398c
1399U
2399d
1400V
2400W
1401V
2401X
1402V
2402Y
1403V
2403Z
1404V
2404a
1405V
2405b
1406V
2406c
1407V
2407d
1408W
2408X
1409W
2409Y
1410W
2410Z
1411W
2411a
1412W
2412b
1413W
2413c
1414W
2414d
1415X
2415Y
1416X
2416Z
1417X
2417a
1418X
2418b
1419X
2419c
1420X
2420d
1421Y
2421Z
1422Y
2422a
1423Y
2423b
1424Y
2424c
1425Y
2425d
1426Z
2426a
1427Z
2427b
1428Z
2428c
1429Z
2429d
1430a
2430b
1431a
2431c
1432a
2432d
1433b
2433c
1434b
2434d
1435c
2435d

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 57
2010B1 - 57
1020A1 - 58
2020C1 - 58
1030A1 - 59
2030D1 - 59
1040A1 - 59
2040E1 - 59
1050A1 - 59
2050F1 - 59
1060A1 - 59
2060G1 - 59
1070A1 - 59
2070H1 - 59
1080A1 - 59
2080I1 - 59
1090A1 - 59
2090J1 - 59
10100A1 - 59
20100K1 - 59
10110A1 - 57
20110L1 - 57
10120A1 - 59
20120M1 - 59
10130A1 - 58
20130N1 - 58
10140A1 - 58
20140O1 - 58
10150A1 - 57
20150P1 - 57
10160A1 - 58
20160Q1 - 58
10170A1 - 58
20170R1 - 58
10180A1 - 59
20180S1 - 59
10190A1 - 56
20190T1 - 56
10200A1 - 56
20200U1 - 56
10210A1 - 56
20210V1 - 56
10220A1 - 58
20220W1 - 58
10230A1 - 58
20230X1 - 58
10240A1 - 58
20240Y1 - 58
10250A1 - 58
20250Z1 - 58
10260A1 - 56
20260a1 - 56
10270A1 - 58
20270b1 - 58
10280A1 - 58
20280c1 - 58
10290A1 - 58
20290d1 - 58
10300B1 - 57
20300C1 - 57
10310B1 - 57
20310D1 - 57
10320B1 - 57
20320E1 - 57
10330B1 - 57
20330F1 - 57
10340B1 - 57
20340G1 - 57
10350B1 - 57
20350H1 - 57
10360B1 - 57
20360I1 - 57
10370B1 - 57
20370J1 - 57
10380B1 - 57
20380K1 - 57
10390B1 - 58
20390L1 - 58
10400B1 - 57
20400M1 - 57
10410B1 - 57
20410N1 - 57
10420B1 - 57
20420O1 - 57
10430B1 - 58
20430P1 - 58
10440B1 - 57
20440Q1 - 57
10450B1 - 57
20450R1 - 57
10460B1 - 57
20460S1 - 57
10470B1 - 56
20470T1 - 56
10480B1 - 56
20480U1 - 56
10490B1 - 56
20490V1 - 56
10500B1 - 57
20500W1 - 57
10510B1 - 57
20510X1 - 57
10520B1 - 57
20520Y1 - 57
10530B1 - 57
20530Z1 - 57
10540B1 - 56
20540a1 - 56
10550B1 - 57
20550b1 - 57
10560B1 - 57
20560c1 - 57
10570B1 - 57
20570d1 - 57
10580C1 - 58
20580D1 - 58
10590C1 - 58
20590E1 - 58
10600C1 - 58
20600F1 - 58
10610C1 - 58
20610G1 - 58
10620C1 - 58
20620H1 - 58
10630C1 - 58
20630I1 - 58
10640C1 - 58
20640J1 - 58
10650C1 - 58
20650K1 - 58
10660C1 - 57
20660L1 - 57
10670C1 - 58
20670M1 - 58
10680C1 - 59
20680N1 - 59
10690C1 - 59
20690O1 - 59
10700C1 - 57
20700P1 - 57
10710C1 - 59
20710Q1 - 59
10720C1 - 59
20720R1 - 59
10730C1 - 58
20730S1 - 58
10740C1 - 56
20740T1 - 56
10750C1 - 56
20750U1 - 56
10760C1 - 56
20760V1 - 56
10770C1 - 59
20770W1 - 59
10780C1 - 59
20780X1 - 59
10790C1 - 59
20790Y1 - 59
10800C1 - 59
20800Z1 - 59
10810C1 - 56
20810a1 - 56
10820C1 - 59
20820b1 - 59
10830C1 - 59
20830c1 - 59
10840C1 - 59
20840d1 - 59
10850D1 - 60
20850E1 - 60
10860D1 - 60
20860F1 - 60
10870D1 - 60
20870G1 - 60
10880D1 - 60
20880H1 - 60
10890D1 - 60
20890I1 - 60
10900D1 - 60
20900J1 - 60
10910D1 - 60
20910K1 - 60
10920D1 - 57
20920L1 - 57
10930D1 - 60
20930M1 - 60
10940D1 - 58
20940N1 - 58
10950D1 - 58
20950O1 - 58
10960D1 - 57
20960P1 - 57
10970D1 - 58
20970Q1 - 58
10980D1 - 58
20980R1 - 58
10990D1 - 60
20990S1 - 60
101000D1 - 56
201000T1 - 56
101010D1 - 56
201010U1 - 56
101020D1 - 56
201020V1 - 56
101030D1 - 58
201030W1 - 58
101040D1 - 58
201040X1 - 58
101050D1 - 58
201050Y1 - 58
101060D1 - 58
201060Z1 - 58
101070D1 - 56
201070a1 - 56
101080D1 - 58
201080b1 - 58
101090D1 - 58
201090c1 - 58
101100D1 - 58
201100d1 - 58
101110E1 - 60
201110F1 - 60
101120E1 - 60
201120G1 - 60
101130E1 - 60
201130H1 - 60
101140E1 - 60
201140I1 - 60
101150E1 - 60
201150J1 - 60
101160E1 - 60
201160K1 - 60
101170E1 - 57
201170L1 - 57
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201600H1 - 60
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101710G1 - 60
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101800G1 - 58
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101820G1 - 58
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101830H1 - 60
201830I1 - 60
101840H1 - 60
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101850H1 - 60
201850K1 - 60
101860H1 - 57
201860L1 - 57
101870H1 - 60
201870M1 - 60
101880H1 - 58
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101900H1 - 57
201900P1 - 57
101910H1 - 58
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101920H1 - 58
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101930H1 - 60
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101960H1 - 56
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102880M1 - 60
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202900U1 - 56
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202960a1 - 56
102970M1 - 58
202970b1 - 58
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102990M1 - 58
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203000O1 - 59
103010N1 - 57
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203060U1 - 56
103070N1 - 56
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103090N1 - 59
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103100N1 - 59
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103120N1 - 56
203120a1 - 56
103130N1 - 59
203130b1 - 59
103140N1 - 59
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203220V1 - 56
103230O1 - 59
203230W1 - 59
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103250O1 - 59
203250Y1 - 59
103260O1 - 59
203260Z1 - 59
103270O1 - 56
203270a1 - 56
103280O1 - 59
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204260a1 - 56
104270Z1 - 59
204270b1 - 59
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204280c1 - 59
104290Z1 - 59
204290d1 - 59
104300a1 - 56
204300b1 - 56
104310a1 - 56
204310c1 - 56
104320a1 - 56
204320d1 - 56
104330b1 - 59
204330c1 - 59
104340b1 - 59
204340d1 - 59
104350c1 - 59
204350d1 - 59

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
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121
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127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
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148
149
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151
152
153
154
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157
158
159
160
161
162
163
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165
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419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435

-
Components

#1: Protein ...
2-hydroxymuconate tautomerase / / 4-oxalocrotonate tautomerase / 4-OT


Mass: 6821.838 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: xylH / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K12 / References: UniProt: Q01468, 2-hydroxymuconate tautomerase
#2: Chemical
ChemComp-7DH / (3E)-5-hydroxy-2-oxopent-3-enoic acid


Mass: 130.099 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C5H6O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM TRIS, pH 8, with 17.5% PEG 4600 (w/v) and 0.1 M potassium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 52302 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 13.7

-
Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data collection
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.06 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.015 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.366
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2535 2666 5.1 %RANDOM
Rwork0.2213 ---
obs0.2229 49580 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 154.75 Å2 / Biso mean: 56.803 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0 Å2-2.49 Å2
2--2.75 Å2-0 Å2
3----1.24 Å2
Refinement stepCycle: final / Resolution: 2.7→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13452 0 72 121 13645
Biso mean--81.36 33.37 -
Num. residues----1772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913662
X-RAY DIFFRACTIONr_bond_other_d0.0110.0213857
X-RAY DIFFRACTIONr_angle_refined_deg1.691.98118307
X-RAY DIFFRACTIONr_angle_other_deg1.921331933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19451746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03323.787544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.267152631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.46115124
X-RAY DIFFRACTIONr_chiral_restr0.0680.22205
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214940
X-RAY DIFFRACTIONr_gen_planes_other0.0130.022720
X-RAY DIFFRACTIONr_mcbond_it4.3765.4237062
X-RAY DIFFRACTIONr_mcbond_other4.3735.4227061
X-RAY DIFFRACTIONr_mcangle_it6.7968.1128776
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A31240.07
12B31240.07
21A31510.08
22C31510.08
31A32160.1
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4272b32180.08
4281Z31880.1
4282c31880.1
4291Z32410.08
4292d32410.08
4301a31260.04
4302b31260.04
4311a30340.09
4312c30340.09
4321a30840.06
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4331b32050.08
4332c32050.08
4341b32900.05
4342d32900.05
4351c32170.08
4352d32170.08
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 206 -
Rwork0.317 3570 -
all-3776 -
obs--98.28 %

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Jul 12, 2017. Major update of PDB

Major update of PDB

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

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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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