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- PDB-3zjc: Crystal structure of GMPPNP-bound human GIMAP7 L100Q variant -

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Basic information

Entry
Database: PDB / ID: 3zjc
TitleCrystal structure of GMPPNP-bound human GIMAP7 L100Q variant
ComponentsGTPASE IMAP FAMILY MEMBER 7
KeywordsHYDROLASE / IMMUNITY
Function / homology
Function and homology information


GTP metabolic process / lipid droplet / GTPase activity / GTP binding / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / identical protein binding
Similarity search - Function
AIG1-type guanine nucleotide-binding (G) domain / GTPase GIMA/IAN/Toc / AIG1 family / AIG1-type G domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase IMAP family member 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsSchwefel, D. / Daumke, O.
CitationJournal: Structure / Year: 2013
Title: Structural Insights Into the Mechanism of Gtpase Activation in the Gimap Family.
Authors: Schwefel, D. / Arasu, B.S. / Marino, S.F. / Lamprecht, B. / Koechert, K. / Rosenbaum, E. / Eichhorst, J. / Wiesner, B. / Behlke, J. / Rocks, O. / Mathas, S. / Daumke, O.
History
DepositionJan 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references / Derived calculations
Revision 1.2Dec 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_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_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_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: GTPASE IMAP FAMILY MEMBER 7
B: GTPASE IMAP FAMILY MEMBER 7
C: GTPASE IMAP FAMILY MEMBER 7
D: GTPASE IMAP FAMILY MEMBER 7
E: GTPASE IMAP FAMILY MEMBER 7
F: GTPASE IMAP FAMILY MEMBER 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,22518
Polymers209,9466
Non-polymers3,27912
Water362
1
A: GTPASE IMAP FAMILY MEMBER 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5383
Polymers34,9911
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPASE IMAP FAMILY MEMBER 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5383
Polymers34,9911
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: GTPASE IMAP FAMILY MEMBER 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5383
Polymers34,9911
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: GTPASE IMAP FAMILY MEMBER 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5383
Polymers34,9911
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: GTPASE IMAP FAMILY MEMBER 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5383
Polymers34,9911
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: GTPASE IMAP FAMILY MEMBER 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5383
Polymers34,9911
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.853, 90.939, 114.551
Angle α, β, γ (deg.)77.30, 85.23, 89.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
GTPASE IMAP FAMILY MEMBER 7 / GIMAP7 / IMMUNITY-ASSOCIATED NUCLEOTIDE 7 PROTEIN / IAN-7


Mass: 34991.066 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8NHV1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.24 Å3/Da / Density % sol: 45.16 % / Description: NONE
Crystal growpH: 7.5 / Details: 19% PEG 3350, 100 MM MOPS PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.09→35 Å / Num. obs: 31271 / % possible obs: 95.3 % / Observed criterion σ(I): 1.5 / Redundancy: 1.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.24
Reflection shellResolution: 3.09→3.28 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.58 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XTN
Resolution: 3.15→32.438 Å / SU ML: 0.51 / σ(F): 1.99 / Phase error: 34.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3052 1481 5 %
Rwork0.2343 --
obs0.2379 29758 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→32.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12423 0 198 2 12623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412779
X-RAY DIFFRACTIONf_angle_d0.92117158
X-RAY DIFFRACTIONf_dihedral_angle_d16.5014898
X-RAY DIFFRACTIONf_chiral_restr0.0531937
X-RAY DIFFRACTIONf_plane_restr0.0032139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.25160.39841220.32042578X-RAY DIFFRACTION94
3.2516-3.36770.36021430.3022549X-RAY DIFFRACTION96
3.3677-3.50240.38551440.28472605X-RAY DIFFRACTION96
3.5024-3.66160.341210.25152588X-RAY DIFFRACTION97
3.6616-3.85430.32151360.23912600X-RAY DIFFRACTION96
3.8543-4.09540.28361400.21162600X-RAY DIFFRACTION97
4.0954-4.41090.30911330.20952570X-RAY DIFFRACTION97
4.4109-4.85340.26351340.19052604X-RAY DIFFRACTION96
4.8534-5.55270.27241380.21192564X-RAY DIFFRACTION96
5.5527-6.98430.3211370.2622559X-RAY DIFFRACTION95
6.9843-32.43990.24521330.20352460X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0109-0.023-0.02390.02580.02460.01760.00370.06690.04960.146-0.01350.0067-0.20010.101100.3161-0.04850.00130.20740.06190.31046.9818-3.26541.9395
20.0144-0.0236-0.00290.02850.0050.00070.08710.0290.184-0.079-0.0905-0.0278-0.01790.015400.3880.00270.00240.30460.02260.3085-0.80161.18585.1264
30.18820.0474-0.01980.0082-0.0150.1329-0.2630.33870.0730.02380.12080.0770.02940.0762-0.02050.21350.01010.05780.32370.03210.234-5.5147-9.417-5.8054
40.2434-0.1093-0.19390.3770.26130.3808-0.26940.11050.0101-0.1351-0.07910.0176-0.2779-0.0479-0.19960.3462-0.1389-0.15290.18120.22550.2737-1.9549-2.1316-11.3708
50.027-0.03010.02150.0244-0.01750.0070.0842-0.03740.007-0.03980.09050.0208-0.04980.0193-00.3849-0.0059-0.06320.3321-0.0450.49321.284125.130113.6651
60.0339-0.00690.03920.0255-0.01020.03210.1531-0.0595-0.0775-0.20080.11250.04720.13530.10010.00220.6903-0.03820.09520.54290.12580.424420.614933.306316.577
70.01470.06520.04440.16350.05050.2085-0.2305-0.0409-0.24820.0958-0.18970.1717-0.11650.048-0.05170.36950.0626-0.10480.3141-0.0340.6468-8.36423.255413.6352
80.0007-0.00290.00150.02610.00130.0032-0.13250.0868-0.1281-0.0287-0.0469-0.06780.0872-0.1018-0.0661-0.01420.02910.27290.3788-0.22490.04921.0245-36.476-3.2202
90.21190.27420.19120.35670.24170.1605-0.15480.01770.2044-0.111-0.10990.2989-0.121-0.133-0.04130.16210.12910.07640.1873-0.05890.2874-2.3259-38.6447-5.6564
100.1818-0.00570.02270.01330.0130.0003-0.1189-0.0075-0.233-0.0394-0.0019-0.1139-0.0065-0.0286-0.0623-0.0824-0.04590.17820.3010.15440.1201-10.0517-37.167-0.0091
110.0055-0.00040.0235-0.00190.00160.0847-0.11-0.0455-0.1825-0.002-0.09430.1331-0.0108-0.0835-0.1686-0.00330.10360.23440.1902-0.00190.2622-4.2769-31.83929.6055
120.0445-0.02910.03370.0378-0.01160.03280.016-0.10810.00630.07720.05380.0865-0.0003-0.08350.0992-0.0760.20750.29150.2958-0.0658-0.03388.9714-26.26078.4777
130.2741-0.0230.07950.09780.09370.163-0.02-0.1123-0.04360.0040.1517-0.0739-0.0679-0.03770.290.05140.06590.35240.02820.1289-0.23446.406-42.36959.2252
140.0049-0.01170.01620.0306-0.01260.05050.1028-0.0158-0.1368-0.10730.06740.00630.0889-0.0059-0.00630.3465-0.1201-0.07340.29010.18710.6813-17.5315-56.52592.0129
150.0940.0619-0.00560.09090.03470.0404-0.0564-0.0645-0.19990.00110.06090.0536-0.0339-0.0760.03890.31230.17940.04110.1324-0.00950.3939-18.8203-43.41990.4965
160.1154-0.05230.02680.0451-0.00560.01330.0182-0.37880.10880.09280.0654-0.0583-0.07180.096-0.03310.10290.00350.10860.2088-0.00430.1535-23.118-10.5102-27.9991
170.11070.03640.02260.11940.01840.02220.07870.03840.1422-0.109-0.0322-0.1442-0.0157-0.00660.11780.03210.08620.16130.094-0.08470.2437-28.6586-10.8233-31.9826
180.01190.00750.00320.01050.01250.0505-0.03090.0178-0.0975-0.043-0.0424-0.05890.1028-0.052-0.023-0.41660.02260.23680.303-0.03950.2822-30.2422-13.9129-39.4235
190.028-0.02250.00370.0675-0.03630.0213-0.02430.03-0.06160.0188-0.01120.0321-0.01050.0144-0.03260.1504-0.01710.1930.6608-0.2910.2539-10.6788-24.7691-40.6372
200.1549-0.05820.01440.01540.01750.1715-0.17540.31160.1188-0.05450.0807-0.02350.0224-0.1617-0.2228-0.1659-0.3520.19440.16980.2110.0251-16.8039-10.7062-41.4443
210.00150.0129-0.05830.0067-0.02120.08230.07340.04690.3646-0.0333-0.10.15180.04040.0427-0.00590.2497-0.01940.04510.1612-0.01960.5895-41.92681.097-33.7529
220.041-0.0646-0.04610.19780.00320.11040.0324-0.0334-0.0541-0.01350.1086-0.0710.06340.14520.13280.41560.2444-0.14820.2991-0.04280.1688-15.9835-42.1709-34.808
230.36110.157-0.10290.1722-0.00380.05750.0763-0.03080.05150.11350.20860.02320.07050.08590.31380.84830.0369-0.09310.0129-0.03270.228-25.3052-44.5836-36.0035
240.11810.00450.03980.1625-0.06890.23970.03590.0129-0.0262-0.14320.08940.11120.2975-0.06570.24880.1872-0.1835-0.22650.1177-0.141-0.5472-28.3629-36.8723-23.9658
250.1747-0.0349-0.08790.1186-0.05250.0386-0.0579-0.0417-0.02580.32550.1208-0.01660.22770.030.18940.72860.043-0.01610.22450.02030.2594-29.6483-48.5788-35.4913
260.08540.0024-0.00810.2331-0.190.1479-0.00260.08140.00650.00310.06470.1729-0.1077-0.08450.08390.2884-0.177-0.03810.39730.09850.215115.82568.162731.9169
270.2908-0.12610.04370.1123-0.12270.279-0.15880.14180.0832-0.14080.04440.0909-0.04650.0525-0.04530.46190.156-0.01240.45690.05370.185913.79648.11238.5388
280.1266-0.04910.020.2547-0.12130.0639-0.0506-0.0406-0.15740.3101-0.1885-0.1038-0.111-0.0937-0.04360.2172-0.0576-0.03370.40490.01560.21657.72626.243543.0067
290.0046-0.0012-0.0015-0.0011-0.0010.0009-0.0404-0.0028-0.0583-0.0837-0.05370.1447-0.02120.0169-0.00010.33630.003-0.17430.43660.06990.37890.1157-7.662827.142
300.1669-0.16960.15140.1562-0.15140.14060.1510.0717-0.0106-0.24310.02640.21390.13310.14190.01130.2967-0.05890.00730.31450.02510.24131.35767.35630.684
310.079-0.11230.00710.1357-0.0117-0.00630.17380.14680.2155-0.052-0.254-0.03890.1506-0.32150.00160.8322-0.13420.08260.48140.05120.326824.407535.945639.4971
320.00740.0107-0.02320.08020.01560.110.0597-0.0564-0.0237-0.00140.00740.0892-0.1410.14450.04820.5092-0.4666-0.07220.49880.05920.338613.85556.062356.618
330.18530.1424-0.07910.1083-0.05340.11350.1928-0.0320.03470.07620.02450.03580.1510.12420.2560.92810.0469-0.37980.2595-0.1670.53589.117-26.990435.0319
340.09870.0021-0.01520.0581-0.0230.02080.13820.4232-0.05980.15010.1110.16610.20420.20470.00820.57970.0593-0.0880.3637-0.05220.272413.7173-21.822444.5257
350.01960.00360.0091-0.00160.01680.0263-0.0113-0.09510.03990.11130.0673-0.07520.13760.1993-0.17950.56230.4433-0.38910.6801-0.28890.442323.8218-23.667637.535
360.0155-0.00550.00310.00370.00460.00790.0213-0.0127-0.0049-0.02120.0116-0.0169-0.09970.0937-0.00360.8408-0.3053-0.09450.27230.12730.77752.3706-46.069251.1448
370.00360.0008-0.0033-0.00050.00040.0008-0.06530.04380.0425-0.0196-0.0747-0.07350.0623-0.0029-0.00010.64790.10550.00820.4299-0.14610.9727-4.146-54.085234.885
380.033-0.03320.05840.0259-0.04740.08260.2041-0.08140.041-0.06140.1297-0.02320.0210.04110.10190.868-0.1615-0.19430.2971-0.04910.60041.0106-28.172355.3394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 8 THROUGH 53 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 54 THROUGH 88 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 89 THROUGH 150 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 151 THROUGH 203 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 204 THROUGH 237 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 238 THROUGH 261 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 262 THROUGH 295 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 7 THROUGH 39 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 40 THROUGH 54 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 55 THROUGH 88 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 89 THROUGH 132 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 133 THROUGH 174 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 175 THROUGH 203 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 204 THROUGH 226 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 227 THROUGH 293 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 8 THROUGH 54 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 55 THROUGH 73 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 74 THROUGH 132 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 133 THROUGH 150 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 151 THROUGH 203 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 204 THROUGH 293 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 9 THROUGH 50 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 51 THROUGH 105 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 106 THROUGH 174 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 175 THROUGH 299 )
26X-RAY DIFFRACTION26CHAIN E AND (RESID 7 THROUGH 54 )
27X-RAY DIFFRACTION27CHAIN E AND (RESID 55 THROUGH 73 )
28X-RAY DIFFRACTION28CHAIN E AND (RESID 74 THROUGH 132 )
29X-RAY DIFFRACTION29CHAIN E AND (RESID 133 THROUGH 150 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 151 THROUGH 203 )
31X-RAY DIFFRACTION31CHAIN E AND (RESID 204 THROUGH 272 )
32X-RAY DIFFRACTION32CHAIN E AND (RESID 273 THROUGH 297 )
33X-RAY DIFFRACTION33CHAIN F AND (RESID 8 THROUGH 73 )
34X-RAY DIFFRACTION34CHAIN F AND (RESID 74 THROUGH 141 )
35X-RAY DIFFRACTION35CHAIN F AND (RESID 142 THROUGH 203 )
36X-RAY DIFFRACTION36CHAIN F AND (RESID 204 THROUGH 226 )
37X-RAY DIFFRACTION37CHAIN F AND (RESID 227 THROUGH 266 )
38X-RAY DIFFRACTION38CHAIN F AND (RESID 267 THROUGH 291 )

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