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- PDB-5v6d: Crystal structure of nucleoside diphosphate kinase from Neisseria... -

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Basic information

Entry
Database: PDB / ID: 5v6d
TitleCrystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / nucleoside diphosphate kinase
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae NCCP11945 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,26154
Polymers263,82216
Non-polymers4,43938
Water39,9752219
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5487
Polymers32,9782
Non-polymers5705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-1 kcal/mol
Surface area12380 Å2
MethodPISA
2
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5487
Polymers32,9782
Non-polymers5705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-0 kcal/mol
Surface area12270 Å2
MethodPISA
3
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4866
Polymers32,9782
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-2 kcal/mol
Surface area12390 Å2
MethodPISA
4
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6108
Polymers32,9782
Non-polymers6336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-5 kcal/mol
Surface area12590 Å2
MethodPISA
5
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4866
Polymers32,9782
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-2 kcal/mol
Surface area12630 Å2
MethodPISA
6
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5487
Polymers32,9782
Non-polymers5705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-0 kcal/mol
Surface area12410 Å2
MethodPISA
7
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5487
Polymers32,9782
Non-polymers5705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint1 kcal/mol
Surface area12470 Å2
MethodPISA
8
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4866
Polymers32,9782
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-4 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.240, 112.350, 112.870
Angle α, β, γ (deg.)104.310, 98.500, 105.390
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleoside diphosphate kinase / NDP kinase / Nucleoside-2-P kinase


Mass: 16488.852 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae NCCP11945 (bacteria)
Gene: ndk, NGK_1320 / Plasmid: NegoA.00438.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4RMG0, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2219 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 17.1 mg/mL NegoA.00438.a.B1.PW37901 + JCSG+ screen B9: 20% PEG6000, 100 mM sodium citrate tribasic, pH 5.0, cryoprotectant: 20% ethylene glycol in two steps, tray 2273617b9, puck mrl5-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 26, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 212120 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 2.972 % / Biso Wilson estimate: 23.07 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.074 / Χ2: 0.992 / Net I/σ(I): 11.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.92.9850.5172.6155070.8910.6396.2
1.9-1.952.9810.3943.26151880.9260.48296.4
1.95-2.012.9850.3164.04148170.9460.38696.4
2.01-2.072.9830.2325.24143290.9690.28496.6
2.07-2.142.9890.1946.1139450.9780.23796.8
2.14-2.212.9830.1617.06135530.9820.19896.7
2.21-2.292.980.1228.65130710.9890.14997
2.29-2.392.9780.1059.87125900.990.12997.1
2.39-2.492.980.09310.88120830.9910.11497.3
2.49-2.622.9730.08212.03115990.9920.10197.5
2.62-2.762.9710.06814.2109680.9940.08397.6
2.76-2.932.9680.05716.43104160.9950.0797.6
2.93-3.132.9650.0518.898550.9950.06197.7
3.13-3.382.9670.04421.1991390.9960.05497.9
3.38-3.72.9540.03823.7383750.9960.04797.9
3.7-4.142.9550.03625.4976360.9960.04597.9
4.14-4.782.9530.03526.9367290.9960.04397.9
4.78-5.852.9390.03626.6956450.9960.04497.9
5.85-8.272.9320.03527.2543790.9960.04397.6
8.27-502.8320.03428.2822960.9960.04394.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3VGS
Resolution: 1.85→44.089 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 1974 0.93 %
Rwork0.15 210063 -
obs0.1504 212037 97.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.95 Å2 / Biso mean: 33.5398 Å2 / Biso min: 11.02 Å2
Refinement stepCycle: final / Resolution: 1.85→44.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17051 0 296 2244 19591
Biso mean--37.96 39.73 -
Num. residues----2245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618124
X-RAY DIFFRACTIONf_angle_d0.75524620
X-RAY DIFFRACTIONf_chiral_restr0.0532822
X-RAY DIFFRACTIONf_plane_restr0.0053241
X-RAY DIFFRACTIONf_dihedral_angle_d15.68111147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89630.32261280.247148051493396
1.8963-1.94750.29661360.2197148671500396
1.9475-2.00480.25491640.2039149341509896
2.0048-2.06960.2591140.1798148921500697
2.0696-2.14350.20381460.1686149811512797
2.1435-2.22930.19881440.1556149671511197
2.2293-2.33080.19541320.1481150151514797
2.3308-2.45370.20661330.1503150001513397
2.4537-2.60740.20411610.1599150921525398
2.6074-2.80870.20381540.1543150631521798
2.8087-3.09130.1791370.1546150731521098
3.0913-3.53840.19721540.1461151681532298
3.5384-4.45730.14451380.1231151611529998
4.4573-44.10140.14371330.1276150451517897
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)
13.4402-1.49040.16073.65422.36882.02950.09170.0239-0.57210.38330.3954-0.91330.2480.3483-0.30120.29660.0232-0.06970.2546-0.09630.5831-5.0666106.304571.9026
23.42081.33422.21762.3473-2.0166.07270.1749-0.44350.0566-0.0586-0.1029-0.90640.34471.0959-0.11270.33740.0078-0.12220.6451-0.17460.70863.1515120.865383.5542
32.79660.05070.29741.6618-0.03242.916-0.0807-0.0115-0.0506-0.00650.4141-0.89-0.00090.4718-0.27450.24390.0047-0.03620.3178-0.12380.6051-1.2496114.455476.3588
43.9724-1.9564-0.37071.8917-0.40152.7349-0.1734-0.5521-0.18620.50350.7807-0.55430.05880.23210.20060.4010.3059-0.36130.5061-0.04371.17220.896100.168478.8396
55.0338-0.4068-0.74860.98380.65350.48710.009-0.03370.4079-0.02670.1491-0.82590.00660.3933-0.48110.55780.1803-0.17210.533-0.39051.714311.9122102.738972.1303
63.4682-0.2724-0.86511.77471.68741.64140.0903-0.1457-0.6380.39090.3355-1.37470.45610.5355-0.22960.39530.0599-0.19310.4556-0.12260.94741.4446109.702178.8324
75.0551-2.6728-2.43396.58182.81966.38420.1792-0.1605-0.28840.5833-0.22870.11320.5311-0.0871-0.0240.4409-0.0371-0.11540.20720.05060.2773-17.2113108.492580.0833
82.63130.5330.76312.69220.13191.0515-0.03020.2648-0.0388-0.72350.2891-0.5585-0.3050.2912-0.20730.3887-0.05040.10820.2076-0.04680.2757-13.2004109.690761.7254
92.43720.86392.7846.5179-3.69086.7320.1145-0.13490.36850.2211-0.360.7152-0.5761-0.3270.12340.3140.0438-0.0380.273-0.10860.378-30.3305111.990769.6163
105.53031.61592.55113.89090.55855.6961-0.16560.1585-0.0487-0.6152-0.11240.5087-0.4501-0.59820.16740.32220.058-0.08220.2404-0.06290.2732-33.0806106.395562.6751
111.5819-0.5641-2.05340.24770.92433.49340.19210.09850.0539-0.66620.1323-0.5714-0.55560.4177-0.33330.4469-0.08050.07970.2149-0.02820.3221-13.8341114.915861.2091
121.3882-0.36520.09754.9587-1.99650.8130.00650.4333-0.0445-0.99920.1204-0.0393-0.65720.3519-0.1040.8627-0.11090.12310.3637-0.03550.2483-15.8972112.099750.622
134.3744-0.4241-2.60999.84143.07684.77370.01710.3825-0.3272-1.36550.15290.2020.3148-0.099-0.26090.84440.01580.01290.35970.01510.3239-19.749399.586349.3364
141.32650.6110.02361.5265-0.44740.62010.02750.14050.0108-1.0915-0.06280.0521-0.4226-0.01190.03770.5260.0308-0.04760.201-0.01630.225-22.5859110.241357.905
155.2419-4.03-2.86577.64734.39636.7417-0.003-0.31270.1666-1.06760.1626-1.086-0.49880.4543-0.19880.4641-0.04190.07890.2254-0.01850.3571-12.5496123.223467.252
167.26840.3144-0.53973.33830.68257.1607-0.09640.29260.6755-0.00070.2155-0.2147-0.4650.1529-0.10230.21160.0247-0.05870.1675-0.00490.2134-4.190280.76564.3149
174.0255-3.3628-1.20523.46270.43422.5612-0.2-0.5121-0.00880.75660.1588-0.08680.24660.04370.01160.45370.0822-0.04060.26260.0380.1643-11.189671.29478.3768
186.56082.35331.46065.3641-4.9487.2715-0.2322-0.23390.36430.51940.19190.0116-0.43190.06610.05850.37040.1157-0.06980.2356-0.03480.2129-10.315984.134675.0721
193.85871.1546-0.21838.8312-2.10283.9605-0.1184-0.07910.12670.18450.2259-0.0964-0.11950.0012-0.11480.17780.0328-0.02420.15240.01440.124-12.073579.042165.0929
207.19311.9106-2.24683.6839-0.41973.2588-0.03780.0631-0.189-0.00540.1751-0.11920.52510.2082-0.13330.33340.0759-0.06120.2398-0.00470.1818-5.342462.156964.1118
215.2224-1.29733.08995.3438-3.55485.438-0.0328-0.0159-0.15920.4358-0.1041-1.01540.33871.37830.10880.33690.1575-0.11570.4866-0.02080.40976.864962.958268.5866
228.9505-2.06230.37972.499-0.88032.8548-0.1778-0.2819-0.32620.54610.1821-0.11230.54010.343-0.03710.40820.1034-0.07930.26810.01770.191-3.933461.988972.4249
235.04835.27-1.56188.3881-2.2663.4414-0.1799-0.00090.33-0.08530.2720.2432-0.10940.0242-0.03890.24850.0362-0.07170.20480.00540.1791-7.184980.812165.8193
245.3115-1.7528-1.19055.1637-3.40733.4756-0.0192-0.00450.35940.21150.2121-0.35950.05890.4481-0.23110.2947-0.0048-0.15990.2832-0.05630.31710.950983.119871.2537
253.84561.54172.27332.2638-1.40744.6181-0.4064-0.71320.52250.87840.1505-0.6254-0.11790.64360.27680.45370.1261-0.1790.4631-0.04190.30893.317778.513282.5773
260.639-0.29380.33510.6872-0.31831.7621-0.0731-0.12590.02070.34220.1213-0.1997-0.01880.2055-0.00890.28410.0556-0.09090.24530.00380.1982-1.111274.290870.2398
272.572-3.04790.09967.76493.5693.8954-0.02-0.00160.0911-0.51450.01010.251-1.1146-0.22770.0110.34750.0226-0.03820.20530.02750.1826-12.296680.611956.4778
282.94770.25730.17573.19790.27982.0823-0.1597-0.32150.01970.4308-0.03680.16940.067-0.13740.1850.2710.05250.01880.18830.00610.153-22.49280.100872.4548
294.2464-0.6551-0.01983.5852-1.93244.12820.12140.34660.1041-0.5506-0.29110.62120.0855-0.17950.22050.27110.0747-0.10380.2267-0.05940.2914-29.355982.165354.5693
302.2075-2.00831.56963.5167-2.79972.2291-0.0543-0.30740.55730.0851-0.2061.4454-0.4977-0.9183-0.16430.35410.1814-0.13140.5009-0.17730.8052-40.774787.414759.3322
312.7386-0.2926-0.00133.6396-0.56963.2953-0.0860.08420.1121-0.0969-0.25190.3267-0.1093-0.20450.25920.18140.054-0.02880.1775-0.04780.1974-27.200183.448363.3067
325.88734.07121.4233.33-0.00122.9598-0.1065-0.8323-0.30050.4291-0.18080.8389-0.3436-0.89880.29510.35410.05730.14670.3767-0.01210.3348-32.523279.192877.7576
333.1981-1.54240.52998.10941.90963.2646-0.4917-0.55910.85740.76640.16830.5305-1.3389-0.01790.28780.66980.10860.06180.4166-0.07670.4183-32.290792.65378.5464
341.53510.06820.52384.43962.00512.3237-0.0426-0.10880.00990.2345-0.26980.618-0.0904-0.28530.29030.19090.04440.02940.2133-0.03120.2838-31.241782.787368.4629
355.88250.46733.65256.20053.24323.6650.1772-0.1549-0.17010.5306-0.0847-0.04120.8004-0.275-0.10320.2811-0.00260.0460.21280.03780.2205-21.961666.215866.7755
362.3924-0.4264-1.04732.5294-0.00283.0667-0.07430.1529-0.0187-0.1868-0.1320.35020.0144-0.25370.15940.1253-0.0107-0.03080.1445-0.00970.1985-23.913655.110743.011
379.1988-1.39593.47014.6547-0.59273.9358-0.19990.10850.2017-0.1754-0.09590.4896-0.1628-0.31380.30140.11790.0173-0.02150.17070.00120.1912-24.652762.832246.1357
384.50272.82070.59216.699-1.38314.61760.0552-0.23550.05970.7772-0.14110.13610.0301-0.25340.07490.33350.03040.03940.16650.02370.1741-19.462454.531362.2138
390.4767-1.19880.65073.0959-1.67120.9017-0.4163-0.411-0.83030.5339-0.05040.9651.3503-0.67320.30120.5417-0.12170.25720.40750.00910.5367-27.387544.288263.2256
403.9197-0.72610.74013.03270.1892.6804-0.1183-0.0609-0.03560.3171-0.14030.3030.1235-0.12810.13960.1456-0.01140.05430.1355-0.01340.1659-22.664453.357653.0024
416.4381-3.659-1.77612.08061.05454.3460.08680.227-0.27510.0578-0.15040.82130.6553-0.5393-0.06250.1677-0.0776-0.02670.2648-0.03630.4831-34.521751.748444.606
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1280.9897-0.83440.81442.7284-0.52342.10930.1347-0.2067-0.16290.4452-0.08570.19840.4433-0.226-0.07470.3207-0.10110.02210.23130.0330.1712-0.7153-35.599311.344
1294.3661-3.7502-2.34233.28922.40523.71890.35970.4109-0.1762-0.8085-0.56340.52590.1145-0.21080.28770.27910.0116-0.05310.2701-0.00410.2001-2.5417-26.0748-4.8507
1301.5662-1.2724-1.35613.1721-0.16931.93380.1683-0.47980.2514-0.1255-0.0272-1.03910.16850.63870.02710.20590.03140.00050.3354-0.03860.415622.3208-28.0903-3.9786
1313.82271.21731.73242.81421.39325.63890.1067-0.0439-0.2304-0.0930.0474-0.39050.54060.1216-0.22260.30260.05210.00640.1557-0.00840.195312.293-38.6093-6.7078
1329.1634-0.72762.51733.13871.274.770.0649-0.1429-0.0729-0.04310.1272-0.39390.22470.336-0.10940.1161-0.00410.00120.1678-0.00690.170713.7365-29.141-1.1116
1333.9383-0.5589-0.11710.11920.09985.5497-0.05840.8349-0.1752-0.9513-0.0074-0.5855-0.28470.339-0.02310.5605-0.02260.20720.3351-0.01820.299312.9617-21.6105-20.7436
1342.76470.30650.51612.63080.35774.00670.06460.1192-0.103-0.58290.0518-0.37510.0082-0.012-0.05450.27950.02320.07090.1502-0.0190.177312.2655-28.0837-12.8918
1356.94713.09242.5563.7715-0.52422.09960.3626-0.0634-0.2903-0.77150.0084-1.0457-0.01510.9546-0.13550.29620.08040.15630.4642-0.10330.547325.5521-34.1555-8.464
1364.1805-0.75761.74219.3473-0.76231.83170.39661.1336-0.9566-2.0253-0.1874-0.2340.79580.687-0.08940.66550.19210.12520.5484-0.06510.550221.3937-42.4376-18.433
1370.52860.04120.36653.21790.50831.31010.02040.2481-0.1579-0.42720.2105-0.58920.08780.2941-0.19330.28050.0110.14080.2859-0.04710.283818.1987-29.7146-13.3107
1383.06270.6474-1.30592.06591.09424.03960.1192-0.2305-0.24170.44260.2335-0.47720.18430.1528-0.19630.2123-0.024-0.02780.26930.01520.297615.4002-21.52783.502
1396.4623-1.86231.51854.4688-0.43135.3682-0.0633-0.86990.33990.8012-0.1581-0.36880.17390.38820.09860.4933-0.0942-0.05790.40830.03040.2633-1.2954-60.2205-11.0175
1405.0175-2.03731.81026.8443-0.46833.6990.1212-0.46840.21430.742-0.31680.9770.2531-0.60860.23150.3641-0.12180.10430.4034-0.10910.3755-17.7647-57.6587-17.489
1412.1294-0.21052.72690.41230.57165.31830.1731-0.54730.47640.6599-0.59920.5599-0.12240.02880.35870.5485-0.1810.12560.3659-0.12460.2807-8.546-50.1121-11.201
1422.9879-1.7821-0.35481.9957-1.21142.26420.2092-0.66440.24180.2734-0.1945-0.08730.2170.08060.03420.3314-0.09590.01110.3451-0.05630.175-2.3432-55.9599-17.3701
1433.2680.22820.04274.8851-0.66434.7416-0.1123-0.0327-0.52130.8227-0.34240.09510.4976-0.10870.30640.5013-0.16170.0440.29420.00720.3014-9.4383-72.7995-20.7252
1444.88410.9872-0.18022.5341-2.31322.22750.0454-1.233-0.91110.98650.00960.90940.4689-0.33250.05090.9941-0.24650.17640.62650.12950.5387-12.8082-77.719-9.2633
1452.0766-0.3179-0.97754.2151-2.47432.10960.1281-0.4022-0.34990.4683-0.20260.73950.9159-0.3923-0.11010.5464-0.25230.0660.4003-0.01510.4302-16.8102-70.8567-17.6094
1464.331-1.45681.95632.0070.55684.24250.1621-0.72950.18610.7034-0.1416-0.1337-0.0083-0.06730.12020.4479-0.169-0.01260.367-0.00960.1731-1.741-57.4814-12.0517
1475.2842-3.62732.84622.7555-0.67597.4676-0.0905-1.1159-0.23321.20370.07270.4030.3890.15690.06240.7625-0.22950.08560.66590.00760.2703-5.9877-58.4342-3.4218
1480.0140.13990.0061.27070.08540.00650.2344-0.07950.02860.7084-0.06960.52970.0269-1.19790.51791.1274-0.31360.51431.0451-0.36060.4307-18.0319-58.8222-1.0486
1493.1418-0.7299-1.30983.29130.83823.09460.2786-0.7591-0.21550.874-0.29890.52610.2633-0.2680.03310.6101-0.23270.07960.47410.01620.3062-9.26-64.3327-9.7876
1504.57-4.7771-4.0238.93262.41934.3190.12-0.22390.15590.33430.0875-0.8713-0.01270.0589-0.16770.3619-0.0496-0.10650.3562-0.00930.30036.0038-58.5498-19.6596
1516.61530.27251.88018.6952.22056.55930.52650.3192-0.4091-0.5545-0.2490.9207-0.0099-0.4442-0.31850.39210.0306-0.06820.2959-0.04330.3079-12.665-47.6681-33.2277
1520.65130.6825-0.41233.55021.08562.3530.151-0.06230.17250.2223-0.3510.5346-0.0801-0.26230.20660.3841-0.00670.01760.289-0.08230.2912-7.2171-44.1909-19.5352
1532.66460.1340.85575.7441.09332.66010.3292-0.1364-0.117-0.1024-0.32030.3802-0.0217-0.21430.01410.3001-0.0127-0.00950.2571-0.07130.1978-8.4544-52.8946-26.2384
1544.79481.8266-0.11194.3635-2.42683.3322-0.06480.51230.2307-0.92080.1363-0.418-0.81480.1478-0.01250.6527-0.06270.1910.3142-0.04550.32987.5097-43.1668-35.9837
1556.5281.04390.78955.23521.00743.53860.19210.05180.0583-0.3603-0.0781-0.1818-0.3242-0.0054-0.13080.29790.00940.03220.1422-0.03460.14080.5178-45.5473-28.849
1566.19674.49812.3613.58991.40181.7116-0.4452-0.32370.8183-1.04610.04830.565-1.1528-0.5290.22740.48660.1148-0.13230.2937-0.08740.4612-13.4102-40.077-31.4098
1571.3102-1.4384-0.88074.30914.00164.0098-0.4595-0.80110.98690.02450.01370.1844-1.5327-0.06230.42860.63870.063-0.12040.4356-0.09890.5517-7.5675-30.1938-25.0272
1581.40290.29390.55434.97152.44992.8723-0.03780.0040.1487-0.3493-0.19120.3001-0.4352-0.10890.24920.41480.0167-0.02040.2217-0.02970.2114-3.7877-41.7693-31.1545
1594.7698-1.7718-1.12037.11865.01543.54730.0512-0.609-0.07460.1593-0.65150.7124-0.1549-0.96030.59080.3831-0.019-0.0240.3782-0.08370.2881-9.8602-59.746-31.896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 40 )A2 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 59 )A41 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 80 )A60 - 80
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 90 )A81 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 102 )A91 - 102
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 132 )A103 - 132
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 141 )A133 - 141
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 40 )B2 - 40
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 50 )B41 - 50
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 71 )B51 - 71
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 80 )B72 - 80
12X-RAY DIFFRACTION12chain 'B' and (resid 81 through 90 )B81 - 90
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 102 )B91 - 102
14X-RAY DIFFRACTION14chain 'B' and (resid 103 through 132 )B103 - 132
15X-RAY DIFFRACTION15chain 'B' and (resid 133 through 141 )B133 - 141
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 10 )C3 - 10
17X-RAY DIFFRACTION17chain 'C' and (resid 11 through 19 )C11 - 19
18X-RAY DIFFRACTION18chain 'C' and (resid 20 through 30 )C20 - 30
19X-RAY DIFFRACTION19chain 'C' and (resid 31 through 40 )C31 - 40
20X-RAY DIFFRACTION20chain 'C' and (resid 41 through 50 )C41 - 50
21X-RAY DIFFRACTION21chain 'C' and (resid 51 through 59 )C51 - 59
22X-RAY DIFFRACTION22chain 'C' and (resid 60 through 71 )C60 - 71
23X-RAY DIFFRACTION23chain 'C' and (resid 72 through 81 )C72 - 81
24X-RAY DIFFRACTION24chain 'C' and (resid 82 through 90 )C82 - 90
25X-RAY DIFFRACTION25chain 'C' and (resid 91 through 102 )C91 - 102
26X-RAY DIFFRACTION26chain 'C' and (resid 103 through 132 )C103 - 132
27X-RAY DIFFRACTION27chain 'C' and (resid 133 through 141 )C133 - 141
28X-RAY DIFFRACTION28chain 'D' and (resid 2 through 40 )D2 - 40
29X-RAY DIFFRACTION29chain 'D' and (resid 41 through 50 )D41 - 50
30X-RAY DIFFRACTION30chain 'D' and (resid 51 through 59 )D51 - 59
31X-RAY DIFFRACTION31chain 'D' and (resid 60 through 80 )D60 - 80
32X-RAY DIFFRACTION32chain 'D' and (resid 81 through 90 )D81 - 90
33X-RAY DIFFRACTION33chain 'D' and (resid 91 through 102 )D91 - 102
34X-RAY DIFFRACTION34chain 'D' and (resid 103 through 132 )D103 - 132
35X-RAY DIFFRACTION35chain 'D' and (resid 133 through 141 )D133 - 141
36X-RAY DIFFRACTION36chain 'E' and (resid 3 through 30 )E3 - 30
37X-RAY DIFFRACTION37chain 'E' and (resid 31 through 40 )E31 - 40
38X-RAY DIFFRACTION38chain 'E' and (resid 41 through 50 )E41 - 50
39X-RAY DIFFRACTION39chain 'E' and (resid 51 through 59 )E51 - 59
40X-RAY DIFFRACTION40chain 'E' and (resid 60 through 81 )E60 - 81
41X-RAY DIFFRACTION41chain 'E' and (resid 82 through 90 )E82 - 90
42X-RAY DIFFRACTION42chain 'E' and (resid 91 through 102 )E91 - 102
43X-RAY DIFFRACTION43chain 'E' and (resid 103 through 132 )E103 - 132
44X-RAY DIFFRACTION44chain 'E' and (resid 133 through 141 )E133 - 141
45X-RAY DIFFRACTION45chain 'F' and (resid 1 through 10 )F1 - 10
46X-RAY DIFFRACTION46chain 'F' and (resid 11 through 19 )F11 - 19
47X-RAY DIFFRACTION47chain 'F' and (resid 20 through 30 )F20 - 30
48X-RAY DIFFRACTION48chain 'F' and (resid 31 through 40 )F31 - 40
49X-RAY DIFFRACTION49chain 'F' and (resid 41 through 50 )F41 - 50
50X-RAY DIFFRACTION50chain 'F' and (resid 51 through 59 )F51 - 59
51X-RAY DIFFRACTION51chain 'F' and (resid 60 through 68 )F60 - 68
52X-RAY DIFFRACTION52chain 'F' and (resid 69 through 80 )F69 - 80
53X-RAY DIFFRACTION53chain 'F' and (resid 81 through 90 )F81 - 90
54X-RAY DIFFRACTION54chain 'F' and (resid 91 through 102 )F91 - 102
55X-RAY DIFFRACTION55chain 'F' and (resid 103 through 132 )F103 - 132
56X-RAY DIFFRACTION56chain 'F' and (resid 133 through 141 )F133 - 141
57X-RAY DIFFRACTION57chain 'G' and (resid 1 through 19 )G1 - 19
58X-RAY DIFFRACTION58chain 'G' and (resid 20 through 30 )G20 - 30
59X-RAY DIFFRACTION59chain 'G' and (resid 31 through 40 )G31 - 40
60X-RAY DIFFRACTION60chain 'G' and (resid 41 through 50 )G41 - 50
61X-RAY DIFFRACTION61chain 'G' and (resid 51 through 59 )G51 - 59
62X-RAY DIFFRACTION62chain 'G' and (resid 60 through 71 )G60 - 71
63X-RAY DIFFRACTION63chain 'G' and (resid 72 through 80 )G72 - 80
64X-RAY DIFFRACTION64chain 'G' and (resid 81 through 90 )G81 - 90
65X-RAY DIFFRACTION65chain 'G' and (resid 91 through 102 )G91 - 102
66X-RAY DIFFRACTION66chain 'G' and (resid 103 through 115 )G103 - 115
67X-RAY DIFFRACTION67chain 'G' and (resid 116 through 132 )G116 - 132
68X-RAY DIFFRACTION68chain 'G' and (resid 133 through 141 )G133 - 141
69X-RAY DIFFRACTION69chain 'H' and (resid 1 through 10 )H1 - 10
70X-RAY DIFFRACTION70chain 'H' and (resid 11 through 30 )H11 - 30
71X-RAY DIFFRACTION71chain 'H' and (resid 31 through 40 )H31 - 40
72X-RAY DIFFRACTION72chain 'H' and (resid 41 through 59 )H41 - 59
73X-RAY DIFFRACTION73chain 'H' and (resid 60 through 80 )H60 - 80
74X-RAY DIFFRACTION74chain 'H' and (resid 81 through 90 )H81 - 90
75X-RAY DIFFRACTION75chain 'H' and (resid 91 through 102 )H91 - 102
76X-RAY DIFFRACTION76chain 'H' and (resid 103 through 132 )H103 - 132
77X-RAY DIFFRACTION77chain 'H' and (resid 133 through 141 )H133 - 141
78X-RAY DIFFRACTION78chain 'I' and (resid 2 through 19 )I2 - 19
79X-RAY DIFFRACTION79chain 'I' and (resid 20 through 30 )I20 - 30
80X-RAY DIFFRACTION80chain 'I' and (resid 31 through 40 )I31 - 40
81X-RAY DIFFRACTION81chain 'I' and (resid 41 through 50 )I41 - 50
82X-RAY DIFFRACTION82chain 'I' and (resid 51 through 59 )I51 - 59
83X-RAY DIFFRACTION83chain 'I' and (resid 60 through 68 )I60 - 68
84X-RAY DIFFRACTION84chain 'I' and (resid 69 through 80 )I69 - 80
85X-RAY DIFFRACTION85chain 'I' and (resid 81 through 90 )I81 - 90
86X-RAY DIFFRACTION86chain 'I' and (resid 91 through 132 )I91 - 132
87X-RAY DIFFRACTION87chain 'I' and (resid 133 through 141 )I133 - 141
88X-RAY DIFFRACTION88chain 'J' and (resid 1 through 10 )J1 - 10
89X-RAY DIFFRACTION89chain 'J' and (resid 11 through 30 )J11 - 30
90X-RAY DIFFRACTION90chain 'J' and (resid 31 through 40 )J31 - 40
91X-RAY DIFFRACTION91chain 'J' and (resid 41 through 50 )J41 - 50
92X-RAY DIFFRACTION92chain 'J' and (resid 51 through 59 )J51 - 59
93X-RAY DIFFRACTION93chain 'J' and (resid 60 through 71 )J60 - 71
94X-RAY DIFFRACTION94chain 'J' and (resid 72 through 80 )J72 - 80
95X-RAY DIFFRACTION95chain 'J' and (resid 81 through 90 )J81 - 90
96X-RAY DIFFRACTION96chain 'J' and (resid 91 through 102 )J91 - 102
97X-RAY DIFFRACTION97chain 'J' and (resid 103 through 132 )J103 - 132
98X-RAY DIFFRACTION98chain 'J' and (resid 133 through 141 )J133 - 141
99X-RAY DIFFRACTION99chain 'K' and (resid 2 through 10 )K2 - 10
100X-RAY DIFFRACTION100chain 'K' and (resid 11 through 19 )K11 - 19
101X-RAY DIFFRACTION101chain 'K' and (resid 20 through 30 )K20 - 30
102X-RAY DIFFRACTION102chain 'K' and (resid 31 through 40 )K31 - 40
103X-RAY DIFFRACTION103chain 'K' and (resid 41 through 50 )K41 - 50
104X-RAY DIFFRACTION104chain 'K' and (resid 51 through 59 )K51 - 59
105X-RAY DIFFRACTION105chain 'K' and (resid 60 through 78 )K60 - 78
106X-RAY DIFFRACTION106chain 'K' and (resid 79 through 90 )K79 - 90
107X-RAY DIFFRACTION107chain 'K' and (resid 91 through 102 )K91 - 102
108X-RAY DIFFRACTION108chain 'K' and (resid 103 through 115 )K103 - 115
109X-RAY DIFFRACTION109chain 'K' and (resid 116 through 132 )K116 - 132
110X-RAY DIFFRACTION110chain 'K' and (resid 133 through 141 )K133 - 141
111X-RAY DIFFRACTION111chain 'L' and (resid 1 through 10 )L1 - 10
112X-RAY DIFFRACTION112chain 'L' and (resid 11 through 30 )L11 - 30
113X-RAY DIFFRACTION113chain 'L' and (resid 31 through 40 )L31 - 40
114X-RAY DIFFRACTION114chain 'L' and (resid 41 through 71 )L41 - 71
115X-RAY DIFFRACTION115chain 'L' and (resid 72 through 90 )L72 - 90
116X-RAY DIFFRACTION116chain 'L' and (resid 91 through 102 )L91 - 102
117X-RAY DIFFRACTION117chain 'L' and (resid 103 through 132 )L103 - 132
118X-RAY DIFFRACTION118chain 'L' and (resid 133 through 141 )L133 - 141
119X-RAY DIFFRACTION119chain 'M' and (resid 1 through 10 )M1 - 10
120X-RAY DIFFRACTION120chain 'M' and (resid 11 through 19 )M11 - 19
121X-RAY DIFFRACTION121chain 'M' and (resid 20 through 30 )M20 - 30
122X-RAY DIFFRACTION122chain 'M' and (resid 31 through 40 )M31 - 40
123X-RAY DIFFRACTION123chain 'M' and (resid 41 through 50 )M41 - 50
124X-RAY DIFFRACTION124chain 'M' and (resid 51 through 59 )M51 - 59
125X-RAY DIFFRACTION125chain 'M' and (resid 60 through 80 )M60 - 80
126X-RAY DIFFRACTION126chain 'M' and (resid 81 through 90 )M81 - 90
127X-RAY DIFFRACTION127chain 'M' and (resid 91 through 102 )M91 - 102
128X-RAY DIFFRACTION128chain 'M' and (resid 103 through 132 )M103 - 132
129X-RAY DIFFRACTION129chain 'M' and (resid 133 through 141 )M133 - 141
130X-RAY DIFFRACTION130chain 'N' and (resid 1 through 10 )N1 - 10
131X-RAY DIFFRACTION131chain 'N' and (resid 11 through 30 )N11 - 30
132X-RAY DIFFRACTION132chain 'N' and (resid 31 through 40 )N31 - 40
133X-RAY DIFFRACTION133chain 'N' and (resid 41 through 59 )N41 - 59
134X-RAY DIFFRACTION134chain 'N' and (resid 60 through 80 )N60 - 80
135X-RAY DIFFRACTION135chain 'N' and (resid 81 through 90 )N81 - 90
136X-RAY DIFFRACTION136chain 'N' and (resid 91 through 102 )N91 - 102
137X-RAY DIFFRACTION137chain 'N' and (resid 103 through 132 )N103 - 132
138X-RAY DIFFRACTION138chain 'N' and (resid 133 through 141 )N133 - 141
139X-RAY DIFFRACTION139chain 'O' and (resid 3 through 10 )O3 - 10
140X-RAY DIFFRACTION140chain 'O' and (resid 11 through 19 )O11 - 19
141X-RAY DIFFRACTION141chain 'O' and (resid 20 through 30 )O20 - 30
142X-RAY DIFFRACTION142chain 'O' and (resid 31 through 40 )O31 - 40
143X-RAY DIFFRACTION143chain 'O' and (resid 41 through 50 )O41 - 50
144X-RAY DIFFRACTION144chain 'O' and (resid 51 through 59 )O51 - 59
145X-RAY DIFFRACTION145chain 'O' and (resid 60 through 71 )O60 - 71
146X-RAY DIFFRACTION146chain 'O' and (resid 72 through 81 )O72 - 81
147X-RAY DIFFRACTION147chain 'O' and (resid 82 through 90 )O82 - 90
148X-RAY DIFFRACTION148chain 'O' and (resid 91 through 102 )O91 - 102
149X-RAY DIFFRACTION149chain 'O' and (resid 103 through 132 )O103 - 132
150X-RAY DIFFRACTION150chain 'O' and (resid 133 through 141 )O133 - 141
151X-RAY DIFFRACTION151chain 'P' and (resid 1 through 10 )P1 - 10
152X-RAY DIFFRACTION152chain 'P' and (resid 11 through 30 )P11 - 30
153X-RAY DIFFRACTION153chain 'P' and (resid 31 through 40 )P31 - 40
154X-RAY DIFFRACTION154chain 'P' and (resid 41 through 59 )P41 - 59
155X-RAY DIFFRACTION155chain 'P' and (resid 60 through 80 )P60 - 80
156X-RAY DIFFRACTION156chain 'P' and (resid 81 through 90 )P81 - 90
157X-RAY DIFFRACTION157chain 'P' and (resid 91 through 102 )P91 - 102
158X-RAY DIFFRACTION158chain 'P' and (resid 103 through 132 )P103 - 132
159X-RAY DIFFRACTION159chain 'P' and (resid 133 through 141 )P133 - 141

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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