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- PDB-9p4d: Crystal Structure of Engineered glutamine binding protein and a G... -

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Basic information

Entry
Database: PDB / ID: 9p4d
TitleCrystal Structure of Engineered glutamine binding protein and a Gd-DOTA ligand - Gln bound
ComponentsAmino acid ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / Amino acid ABC transporter / substrate binding protein
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / amino acid transport / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Glutamine-binding periplasmic protein GlnH, type 2 periplasmic binding protein fold / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins.
Similarity search - Domain/homology
: / ACETATE ION / GADOLINIUM ION / GLUTAMINE / Glutamine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsBruchs, A.T. / Wilson, C.A. / Boggs, D.G. / Fatima, S. / Bridwell-Rabb, J. / Olshansky, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138138 United States
CitationJournal: Chem Sci / Year: 2025
Title: Development of a glutamine-responsive MRI contrast agent.
Authors: Wilson, C.A. / Bruchs, A.T. / Fatima, S. / Boggs, D.G. / Bridwell-Rabb, J. / Olshansky, L.
History
DepositionJun 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amino acid ABC transporter substrate-binding protein
B: Amino acid ABC transporter substrate-binding protein
C: Amino acid ABC transporter substrate-binding protein
D: Amino acid ABC transporter substrate-binding protein
E: Amino acid ABC transporter substrate-binding protein
F: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,62349
Polymers151,5286
Non-polymers7,09543
Water6,179343
1
A: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4709
Polymers25,2551
Non-polymers1,2158
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5409
Polymers25,2551
Non-polymers1,2858
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,62511
Polymers25,2551
Non-polymers1,37010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2936
Polymers25,2551
Non-polymers1,0385
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3487
Polymers25,2551
Non-polymers1,0936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Amino acid ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3487
Polymers25,2551
Non-polymers1,0936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)221.437, 221.437, 79.558
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 19 or resid 21 through 71 or resid 73 through 222 or resid 301))
d_2ens_1(chain "B" and (resid 4 through 19 or resid 21 through 71 or resid 73 through 222 or resid 301))
d_3ens_1(chain "C" and (resid 4 through 19 or resid 21 through 71 or resid 73 through 222 or resid 301))
d_4ens_1(chain "D" and (resid 4 through 19 or resid 21 through 71 or resid 73 through 222 or resid 301))
d_5ens_1(chain "E" and (resid 4 through 19 or resid 21 through 71 or resid 73 through 222 or resid 301))
d_6ens_1(chain "F" and (resid 4 through 19 or resid 21 through 71 or resid 73 through 222 or resid 301))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSLYSLYSAA4 - 197 - 22
d_12GLYGLYILEILEAA21 - 7124 - 74
d_13ASPASPGLYGLYAA73 - 22276 - 225
d_14GLNGLNGLNGLNAG301
d_21LYSLYSLYSLYSBB4 - 197 - 22
d_22GLYGLYILEILEBB21 - 7124 - 74
d_23ASPASPGLYGLYBB73 - 22276 - 225
d_24GLNGLNGLNGLNBO301
d_31LYSLYSLYSLYSCC4 - 197 - 22
d_32GLYGLYILEILECC21 - 7124 - 74
d_33ASPASPGLYGLYCC73 - 22276 - 225
d_34GLNGLNGLNGLNCW301
d_41LYSLYSLYSLYSDD4 - 197 - 22
d_42GLYGLYILEILEDD21 - 7124 - 74
d_43ASPASPGLYGLYDD73 - 22276 - 225
d_44GLNGLNGLNGLNDGA301
d_51LYSLYSLYSLYSEE4 - 197 - 22
d_52GLYGLYILEILEEE21 - 7124 - 74
d_53ASPASPGLYGLYEE73 - 22276 - 225
d_54GLNGLNGLNGLNEMA402
d_61LYSLYSLYSLYSFF4 - 197 - 22
d_62GLYGLYILEILEFF21 - 7124 - 74
d_63ASPASPGLYGLYFF73 - 22276 - 225
d_64GLNGLNGLNGLNFRA301

NCS oper:
IDCodeMatrixVector
1given(-0.747131872534, -0.583983815743, -0.317422223535), (0.510044413514, -0.197496562559, -0.837167727532), (0.426202605913, -0.787374123735, 0.445413659406)-43.3221387275, -60.2864722341, -24.6796601981
2given(-0.992520462748, 0.122050390389, -0.00261404534739), (0.122052471704, 0.992523435368, -0.000651457205904), (0.0025149906621, -0.000965635303261, -0.999996371179)0.431419830199, 0.120122762619, 39.2879891908
3given(0.800811152718, 0.557371468976, 0.219176967891), (0.419142939855, -0.260155686328, -0.869849535748), (-0.427809179019, 0.788451688084, -0.441953891153)35.9042480551, -64.5320665555, 64.062430175
4given(0.615269656738, 0.639552032276, -0.460886588554), (0.683077137405, -0.14068223447, 0.716668775139), (0.393508416494, -0.755765642853, -0.52342088154)78.262302503, -140.296646214, 9.50167415636
5given(-0.529290685553, -0.65859155288, 0.534891144684), (0.738778237338, -0.0477459698739, 0.672255188449), (-0.417202692013, 0.750984346598, 0.511824603689)-94.3349673556, -129.247204858, 30.405124962

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Amino acid ABC transporter substrate-binding protein / Glutamine ABC transporter substrate-binding protein GlnH / Glutamine ABC transporter substrate- ...Glutamine ABC transporter substrate-binding protein GlnH / Glutamine ABC transporter substrate-bindnig protein / Glutamine ABC transporter / periplasmic glutamine-binding protein (TC 3.A.1.3.2) / substrate-binding protein / Glutamine-binding periplasmic protein / Periplasmic glutamine-binding protein / Periplasmic glutamine-binding protein permease / Permease of periplasmic glutamine-binding protein


Mass: 25254.658 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: glnH, A5U30_004091, A6592_04880, A8499_000176, A9X72_16950, AAG43_003583, ACN68_16860, ACN81_02400, ACU57_05845, AF998_000125, AM464_21485, APX88_17575, AT335_000554, AT845_002764, AW118_24500, ...Gene: glnH, A5U30_004091, A6592_04880, A8499_000176, A9X72_16950, AAG43_003583, ACN68_16860, ACN81_02400, ACU57_05845, AF998_000125, AM464_21485, APX88_17575, AT335_000554, AT845_002764, AW118_24500, AW119_03915, AWP47_29145, B6R12_003536, B6R15_002883, B6R31_003222, B6R48_003973, B6R87_003886, BANRA_01322, BANRA_01764, BEA19_14205, BER14_07540, BF481_003043, BG944_004267, BGM66_000966, BHS81_04935, BJI68_11495, BJJ90_17825, BK292_21345, BK383_19105, BLM69_000575, BMC79_000611, BMT49_05685, BMT50_00560, BMT91_20520, BN17_06101, BO068_000746, BOH76_16995, BON63_24725, BON64_24190, BON65_04740, BON66_07455, BON67_25290, BON68_02720, BON69_08400, BON70_24775, BON71_14305, BON72_22420, BON73_01195, BON74_14830, BON75_15470, BON76_25420, BON77_09375, BON78_20655, BON79_20060, BON80_12630, BON81_19085, BON82_15305, BON83_05500, BON84_13940, BON86_21740, BON87_16800, BON88_07465, BON89_22820, BON90_14295, BON91_21900, BON92_22285, BON93_04225, BON94_25770, BON95_05775, BON96_27115, BON97_10525, BON98_19710, BR158_002878, BRV02_000648, BSR05_11095, BTB68_001717, BTQ06_26205, BUO55_004168, BvCmsF30A_02312, BvCmsHHP019_04964, BvCmsKKP061_03133, BvCmsKSNP073_02686, BVL39_24445, BXT93_09325, BZL69_00955, C0P57_004641, C1Q91_004053, C2121_002453, C2M16_01565, C2R31_002978, C2U48_05980, C3F40_08525, C5N07_02720, C5Y87_11455, C9114_21285, C9160_24490, C9E67_21255, C9Z68_13890, CA593_25060, CCS08_19690, CCV12_002704, CDC27_03365, CDL36_05995, CDL37_06170, CF22_003152, CG831_000699, CHM61_001352, CIG67_24135, CO706_26845, CQ986_002219, CR538_17365, CR539_08495, CR628_003110, CTR35_001347, CV83915_00768, CWS33_06680, CX938_000617, CXJ73_000498, CY655_04230, D0X26_05085, D1912_20655, D1H34_001169, D3822_09995, D3C88_05045, D3G36_03255, D3Y67_17015, D4N09_12520, D4U49_00030, D9D43_04855, D9D77_09815, D9E34_09280, D9E49_16110, D9H94_11690, D9J03_11000, D9J61_05355, DAH17_03825, DAH18_19240, DAH19_07490, DAH20_21020, DAH21_16625, DAH22_20195, DAH23_12545, DAH24_12625, DAH25_13880, DAH26_12570, DAH27_27195, DAH28_26570, DAH29_21215, DAH30_24830, DAH31_23660, DAH32_25755, DAH33_16740, DAH34_00565, DAH35_19590, DAH36_01785, DAH37_00035, DAH38_23920, DAH40_16855, DAH41_26115, DAH42_14420, DAH43_13740, DAH45_14115, DAH46_16030, DAH47_10645, DAH48_08930, DAH49_15255, DAH50_02775, DD762_19985, DEN86_16580, DEN87_25365, DEN88_18460, DEN89_18240, DEN90_15895, DEN91_18520, DEN92_25370, DEN93_25685, DEN94_25170, DEN95_25645, DEN96_14460, DEN97_05945, DEN98_14610, DEN99_03305, DEO00_15605, DEO01_16930, DEO02_15845, DEO03_02745, DEO04_17445, DEO05_17315, DEO06_16065, DEO07_16850, DEO08_10875, DEO09_17170, DEO10_17430, DEO11_17320, DEO12_17235, DEO13_25310, DEO14_25015, DEO15_18570, DEO17_18420, DEO18_14095, DEO19_25855, DEO20_09480, DIV22_24420, DKP82_24310, DM870_16080, DN627_03140, DNX30_21735, DRW19_18320, DS732_09030, DTL43_10730, DTL90_03445, DTM45_05760, DU321_00670, DXT69_17235, DXT70_03865, DXT71_08710, DXT73_10050, E0I42_20880, E2112_02675, E2113_01945, E2114_18730, E2115_17055, E2116_04330, E2117_24095, E2118_16300, E2119_12420, E2120_04215, E2121_18185, E2122_15175, E2123_15570, E2124_10840, E2125_18565, E2127_00470, E2128_04955, E2129_10405, E2130_05520, E2131_16230, E2132_01450, E2133_04840, E2134_04965, E2135_16085, E2136_14980, E2646_20010, E3O05_01530, E4K51_02810, E4T14_00550, E4T84_17465, E5H86_25390, E5M02_22525, E5P22_03440, E5P23_09650, E5P24_07820, E5P25_14380, E5P26_02375, E5P27_03730, E5P28_05135, E5P29_02255, E5P30_11875, E5P31_05030, E5P32_00405, E5P33_13470, E5P34_03095, E5P35_02485, E5P36_15665, E5P37_20315, E5P39_19970, E5P40_02695, E5P41_16665, E5P42_12050, E5P43_17005, E5P44_18530, E5P45_22380, E5P46_16045, E5P47_19935, E5P48_15405, E5P49_19430, E5P50_22740, E5P51_16920, E5S34_18760, E5S35_18835, E5S36_04930, E5S37_23235, E5S38_16415, E5S39_18510, E5S43_19010, E5S44_19440, E5S45_23380, E5S46_22040, E5S47_18610, E5S48_18775, E5S51_14615, E5S52_10650, E5S53_16880, E5S54_25355, E5S55_16870, E5S56_20090, E5S57_09335, E5S58_12745, E5S61_14780, E5S62_04320, E6C80_01100, E6D34_16620, EA239_02055, EA435_03075, EAI46_17535, EAN77_08520, EAX79_16230, EC1094V2_3069, EC95NR1_05084, ECs0889, ED648_06680, EHD79_17160, EI021_00555, EIA08_01310, EIZ93_04910, EKI52_06410, EL79_3071, EL80_3032, ELT16_02415, ELT17_17330, ELT20_02820, ELT21_01480, ELT22_07560, ELT23_02015, ELT24_02785, ELT25_04925, ELT26_09185, ELT27_07495, ELT28_15430, ELT29_09190, ELT30_04155, ELT31_02235, ELT32_01320, ELT33_01125, ELT34_02155, ELT35_01150, ELT36_07860, ELT38_02015, ELT39_12720, ELT40_06625, ELT41_10995, ELT44_00485, ELT45_07655, ELT46_05645, ELT48_02765, ELT49_11575, ELT50_00370, ELT51_04720, ELT52_01735, ELT54_03790, ELT55_02630, ELT56_04370, ELT58_13405, ELT59_01975, ELT60_02685, ELT61_00525, ELT63_00400, ELT72_09395, ELU07_01290, ELU82_01275, ELU83_00030, ELU85_01090, ELU88_02755, ELU89_06090, ELU90_16660, ELU91_09660, ELU94_20245, ELU95_04135, ELU96_01710, ELU97_02075, ELU98_07325, ELU99_17975, ELV00_00990, ELV01_02685, ELV02_04500, ELV03_02685, ELV04_09130, ELV05_01070, ELV07_02685, ELV08_05490, ELV09_09705, ELV10_03635, ELV11_00495, ELV12_17700, ELV13_05135, ELV15_08005, ELV16_06920, ELV20_01690, ELV21_07280, ELV22_03390, ELV23_04940, ELV26_19830, ELV28_13395, ELV29_14030, ELV40_13070, ELX48_20960, ELX61_08885, ELX66_13645, ELX68_03535, ELX69_04805, ELX76_06605, ELX79_08650, ELX85_04825, ELX96_24945, ELY02_21695, ELY32_15660, ELY36_07870, ELY39_10000, ELY41_22740, ELY48_10875, EN85_004581, ERS085406_04011, ERS139208_02685, EWK56_11475, ExPECSC038_02876, EXX13_17615, EYV17_11920, EYV18_03835, F0L67_04275, F2N20_02135, F2N31_03410, F3N40_12265, F7F11_11485, F7N46_08470, F9413_07780, F9461_01305, F9B07_02710, F9S83_08475, F9V24_04485, F9X20_12650, FDM60_08540, FE584_14605, FE587_14715, FEJ01_13600, FFF58_04660, FGG80_18845, FHO90_02740, FHQ91_05095, FIJ20_11900, FJQ40_17745, FJQ51_03360, FJQ53_08590, FKO60_07285, FOI11_009340, FOI11_10705, FPI65_04950, FPJ29_13820, FPS11_01585, FQF29_02765, FV293_02200, FVB16_07150, FWK02_14955, FY127_05225, FZC17_24290, FZN31_16475, FZU14_07000, G3813_001838, G3V95_03410, G3W53_12740, G4A38_09725, G4A47_02555, G5603_02180, G7630_000206, G9448_06715, GAI66_11760, GAI89_13630, GAJ12_17235, GAJ26_02185, GF147_05165, GF699_09700, GFY34_01840, GIB53_03185, GJ11_04510, GJO56_05855, GKF66_09425, GKF89_13835, GNW61_02415, GNZ05_09120, GOP25_10140, GP711_00870, GP944_02795, GP965_17210, GP979_15650, GQM04_08380, GQM13_17840, GQM21_08920, GQN34_06325, GQW07_06480, GQW68_09320, GQW80_16390, GRC73_03245, GRO95_00200, GRW05_01550, GRW24_15895, GRW56_11730, GRW57_13110, GSM54_17415, GSY44_21500, GTP88_11170, GUC01_03260, GUI33_12255, H0O37_11575, H0O39_10830, H0O72_02630, HEP30_007075, HEP34_000682, HHH44_004674, HI055_001651, HIE29_000308, HIN64_003897, HJQ60_003183, HJU54_001291, HKA49_004171, HL563_07185, HL601_10425, HLV18_05320, HLX92_21635, HLZ50_00225, HmCms169_02183, HMJ82_04430, HMV95_02550, HMW38_01730, HNC36_00575, HNC59_02155, HNC66_13445, HNC99_06490, HND12_01310, HV109_16015, HV209_04855, HVV39_21020, HVW04_06960, HVW19_18030, HVW43_08305, HVY77_17775, HVZ71_16640, HX136_17495, I6H00_09980, I6H01_21610, I6H02_22350, IA00_002027, IFB95_003951, IH768_00950, IH772_11995, IT029_003785, J0541_000988, J4S20_005071, J5U05_002124, JE86ST02C_09210, JE86ST05C_09750, JFD_02409, JNP96_08670, NCTC10082_05067, NCTC10089_03418, NCTC10090_00382, NCTC10418_05048, NCTC10429_05756, NCTC10865_04252, NCTC11181_00607, NCTC12950_03687, NCTC13127_04610, NCTC13216_03355, NCTC4450_03842, NCTC7922_06781, NCTC7927_03810, NCTC7928_05513, NCTC8008_02951, NCTC8009_06196, NCTC8179_02263, NCTC8333_03962, NCTC8450_01827, NCTC8500_03700, NCTC8621_03555, NCTC8959_00379, NCTC8960_00488, NCTC9001_01370, NCTC9036_03440, NCTC9037_03540, NCTC9075_04560, NCTC9111_03455, NCTC9702_03882, NCTC9706_00702, NCTC9775_01675, NCTC9777_03409, NCTC9962_02368, ND22_002874, RG28_00455, SAMEA3472044_00248, SAMEA3472056_00231, SAMEA3472147_02754, SAMEA3751407_00314, SAMEA3752557_02233, SAMEA3753106_00906, TUM18780_29030, WP4S18E07_30170, WR15_25350, XU56_002013
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3THM2

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Non-polymers , 7 types, 386 molecules

#2: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-A1C21 / 4-oxo-4-[(2-{2-[4,7,10-tris(carboxymethyl)-1,4,7,10-tetraazacyclododecan-1-yl]acetamido}ethyl)amino]butanoic acid


Mass: 546.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H38N6O10 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GD3 / GADOLINIUM ION


Mass: 157.250 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Gd / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 4.6
Details: 0.17 M Ammonium Sulfate, 0.1 M Sodium Acetate, 25% W/V PEG-MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.57→40 Å / Num. obs: 70746 / % possible obs: 99.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 52.08 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.124 / Net I/σ(I): 14.79
Reflection shellResolution: 2.57→2.66 Å / Num. unique obs: 6979 / CC1/2: 0.886 / Rrim(I) all: 0.934

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→38.5 Å / SU ML: 0.3609 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2344 3549 5.02 %
Rwork0.2113 67196 -
obs0.2125 70745 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.89 Å2
Refinement stepCycle: LAST / Resolution: 2.57→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10455 0 418 343 11216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012111303
X-RAY DIFFRACTIONf_angle_d2.4815201
X-RAY DIFFRACTIONf_chiral_restr0.0961611
X-RAY DIFFRACTIONf_plane_restr0.00731950
X-RAY DIFFRACTIONf_dihedral_angle_d17.94944302
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.81169141096
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.641351477905
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.816896296486
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS1.05620391912
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS1.04024717609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.610.3341400.3162607X-RAY DIFFRACTION97.93
2.61-2.640.34511430.30472709X-RAY DIFFRACTION99.62
2.64-2.680.32611390.28682611X-RAY DIFFRACTION99.82
2.68-2.730.29781410.28622702X-RAY DIFFRACTION99.75
2.73-2.770.31661450.26922671X-RAY DIFFRACTION99.93
2.77-2.820.28681410.26142657X-RAY DIFFRACTION99.93
2.82-2.870.30531390.26632709X-RAY DIFFRACTION100
2.87-2.920.27741430.25452671X-RAY DIFFRACTION100
2.92-2.980.33181400.2712677X-RAY DIFFRACTION99.96
2.98-3.050.29551430.26112694X-RAY DIFFRACTION99.89
3.05-3.120.31031410.24712679X-RAY DIFFRACTION99.86
3.12-3.20.32561400.23832675X-RAY DIFFRACTION99.93
3.2-3.280.25521400.23322691X-RAY DIFFRACTION99.61
3.28-3.380.26521300.22842652X-RAY DIFFRACTION99.39
3.38-3.490.2451420.21812707X-RAY DIFFRACTION99.58
3.49-3.610.23781410.21312715X-RAY DIFFRACTION99.62
3.61-3.760.21841420.19422658X-RAY DIFFRACTION99.47
3.76-3.930.22511450.18482677X-RAY DIFFRACTION99.68
3.93-4.140.18751440.18152697X-RAY DIFFRACTION99.75
4.14-4.390.18591460.17452696X-RAY DIFFRACTION99.79
4.4-4.730.17851360.16292701X-RAY DIFFRACTION99.51
4.73-5.210.17951480.17542692X-RAY DIFFRACTION99.47
5.21-5.960.24091470.20052703X-RAY DIFFRACTION99.55
5.96-7.50.23161440.22642745X-RAY DIFFRACTION99.79
7.5-38.50.20051490.1962800X-RAY DIFFRACTION99.16

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