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- PDB-6phe: Crystal structure of Methylglyoxal synthase from Elizabethkingia ... -

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Basic information

Entry
Database: PDB / ID: 6phe
TitleCrystal structure of Methylglyoxal synthase from Elizabethkingia anophelis NUHP1
ComponentsMethylglyoxal synthase
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / NUHP1
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity
Similarity search - Function
Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Rossmann fold ...Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Methylglyoxal synthase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Methylglyoxal synthase from Elizabethkingia anophelis NUHP1
Authors: Abendroth, J. / Fox III, D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylglyoxal synthase
B: Methylglyoxal synthase
C: Methylglyoxal synthase
D: Methylglyoxal synthase
E: Methylglyoxal synthase
F: Methylglyoxal synthase
G: Methylglyoxal synthase
H: Methylglyoxal synthase
I: Methylglyoxal synthase
J: Methylglyoxal synthase
K: Methylglyoxal synthase
L: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,04826
Polymers219,67212
Non-polymers1,37614
Water22,1761231
1
A: Methylglyoxal synthase
B: Methylglyoxal synthase
C: Methylglyoxal synthase
D: Methylglyoxal synthase
E: Methylglyoxal synthase
F: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,64214
Polymers109,8366
Non-polymers8068
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21290 Å2
ΔGint-176 kcal/mol
Surface area31050 Å2
MethodPISA
2
G: Methylglyoxal synthase
H: Methylglyoxal synthase
I: Methylglyoxal synthase
J: Methylglyoxal synthase
K: Methylglyoxal synthase
L: Methylglyoxal synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,40612
Polymers109,8366
Non-polymers5706
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21160 Å2
ΔGint-166 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.590, 167.590, 159.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 or (resid 4 and (name...
21(chain B and (resid 3 or (resid 4 and (name...
31(chain C and (resid 3 or (resid 4 and (name...
41(chain D and (resid 3 through 4 or resid 6...
51(chain E and (resid 3 or (resid 4 and (name...
61(chain F and (resid 3 or (resid 4 and (name...
71(chain G and (resid 3 or (resid 4 and (name...
81(chain H and (resid 3 or (resid 4 and (name...
91(chain I and (resid 3 or (resid 4 and (name...
101(chain J and (resid 3 or (resid 4 and (name...
111(chain K and (resid 3 or (resid 4 and (name...
121(chain L and (resid 3 or (resid 4 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 or (resid 4 and (name...A3
121(chain A and (resid 3 or (resid 4 and (name...A4
131(chain A and (resid 3 or (resid 4 and (name...A3 - 200
141(chain A and (resid 3 or (resid 4 and (name...A3 - 200
151(chain A and (resid 3 or (resid 4 and (name...A3 - 200
161(chain A and (resid 3 or (resid 4 and (name...A3 - 200
211(chain B and (resid 3 or (resid 4 and (name...B3
221(chain B and (resid 3 or (resid 4 and (name...B4
231(chain B and (resid 3 or (resid 4 and (name...B2 - 200
241(chain B and (resid 3 or (resid 4 and (name...B2 - 200
251(chain B and (resid 3 or (resid 4 and (name...B2 - 200
261(chain B and (resid 3 or (resid 4 and (name...B2 - 200
311(chain C and (resid 3 or (resid 4 and (name...C3
321(chain C and (resid 3 or (resid 4 and (name...C4
331(chain C and (resid 3 or (resid 4 and (name...C2 - 200
341(chain C and (resid 3 or (resid 4 and (name...C2 - 200
351(chain C and (resid 3 or (resid 4 and (name...C2 - 200
361(chain C and (resid 3 or (resid 4 and (name...C2 - 200
411(chain D and (resid 3 through 4 or resid 6...D3 - 4
421(chain D and (resid 3 through 4 or resid 6...D6 - 8
431(chain D and (resid 3 through 4 or resid 6...D11 - 26
441(chain D and (resid 3 through 4 or resid 6...D3 - 200
451(chain D and (resid 3 through 4 or resid 6...D3 - 200
461(chain D and (resid 3 through 4 or resid 6...D3 - 200
471(chain D and (resid 3 through 4 or resid 6...D3 - 200
481(chain D and (resid 3 through 4 or resid 6...D3 - 200
491(chain D and (resid 3 through 4 or resid 6...D3 - 200
4101(chain D and (resid 3 through 4 or resid 6...D3 - 200
511(chain E and (resid 3 or (resid 4 and (name...E3
521(chain E and (resid 3 or (resid 4 and (name...E4
531(chain E and (resid 3 or (resid 4 and (name...E2 - 200
541(chain E and (resid 3 or (resid 4 and (name...E2 - 200
551(chain E and (resid 3 or (resid 4 and (name...E2 - 200
561(chain E and (resid 3 or (resid 4 and (name...E2 - 200
611(chain F and (resid 3 or (resid 4 and (name...F3
621(chain F and (resid 3 or (resid 4 and (name...F4
631(chain F and (resid 3 or (resid 4 and (name...F2 - 200
641(chain F and (resid 3 or (resid 4 and (name...F2 - 200
651(chain F and (resid 3 or (resid 4 and (name...F2 - 200
661(chain F and (resid 3 or (resid 4 and (name...F2 - 200
711(chain G and (resid 3 or (resid 4 and (name...G3
721(chain G and (resid 3 or (resid 4 and (name...G4
731(chain G and (resid 3 or (resid 4 and (name...G2 - 200
741(chain G and (resid 3 or (resid 4 and (name...G2 - 200
751(chain G and (resid 3 or (resid 4 and (name...G2 - 200
761(chain G and (resid 3 or (resid 4 and (name...G2 - 200
811(chain H and (resid 3 or (resid 4 and (name...H3
821(chain H and (resid 3 or (resid 4 and (name...H4
831(chain H and (resid 3 or (resid 4 and (name...H3 - 200
841(chain H and (resid 3 or (resid 4 and (name...H3 - 200
851(chain H and (resid 3 or (resid 4 and (name...H3 - 200
861(chain H and (resid 3 or (resid 4 and (name...H3 - 200
911(chain I and (resid 3 or (resid 4 and (name...I3
921(chain I and (resid 3 or (resid 4 and (name...I4
931(chain I and (resid 3 or (resid 4 and (name...I3 - 200
941(chain I and (resid 3 or (resid 4 and (name...I3 - 200
951(chain I and (resid 3 or (resid 4 and (name...I3 - 200
961(chain I and (resid 3 or (resid 4 and (name...I3 - 200
1011(chain J and (resid 3 or (resid 4 and (name...J3
1021(chain J and (resid 3 or (resid 4 and (name...J4
1031(chain J and (resid 3 or (resid 4 and (name...J3 - 200
1041(chain J and (resid 3 or (resid 4 and (name...J3 - 200
1051(chain J and (resid 3 or (resid 4 and (name...J3 - 200
1061(chain J and (resid 3 or (resid 4 and (name...J3 - 200
1111(chain K and (resid 3 or (resid 4 and (name...K3
1121(chain K and (resid 3 or (resid 4 and (name...K4
1131(chain K and (resid 3 or (resid 4 and (name...K3 - 200
1141(chain K and (resid 3 or (resid 4 and (name...K3 - 200
1151(chain K and (resid 3 or (resid 4 and (name...K3 - 200
1161(chain K and (resid 3 or (resid 4 and (name...K3 - 200
1211(chain L and (resid 3 or (resid 4 and (name...L3
1221(chain L and (resid 3 or (resid 4 and (name...L4
1231(chain L and (resid 3 or (resid 4 and (name...L3 - 200
1241(chain L and (resid 3 or (resid 4 and (name...L3 - 200
1251(chain L and (resid 3 or (resid 4 and (name...L3 - 200
1261(chain L and (resid 3 or (resid 4 and (name...L3 - 200

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Components

#1: Protein
Methylglyoxal synthase / / MGS


Mass: 18305.998 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: mgsA, BD94_2272 / Plasmid: ElanA.00692.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A077EEZ5, methylglyoxal synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Rigaku Reagents JCSG+ screen, condition a11: 50% (V/V) MPD, 200mM ammonium phosphate monobasic, Tris base / HCl pH 8.5. ElanA.00692.a.B1.PS38386 at 18.2mg/ml: cryo: direct: tray: 2978372 a11: puck vsf3-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→48.61 Å / Num. obs: 132174 / % possible obs: 99.9 % / Redundancy: 9.996 % / Biso Wilson estimate: 29.637 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.107 / Χ2: 1.014 / Net I/σ(I): 19.3 / Num. measured all: 1321165 / Scaling rejects: 28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.1510.0420.5594.596838964596430.9280.588100
2.15-2.2110.050.4485.694739942794270.9520.471100
2.21-2.2810.0520.3796.6692161916991680.9650.399100
2.28-2.3510.0580.3247.789695891889180.9730.341100
2.35-2.4210.0630.3128.187240867086690.9740.329100
2.42-2.5110.070.259.9484053834783470.9840.263100
2.51-2.610.0520.23110.6781532811181110.9850.243100
2.6-2.7110.0590.18812.8678396779577940.9910.198100
2.71-2.8310.0580.16614.4875244748174810.9920.175100
2.83-2.9710.0390.13317.7272182719071900.9950.14100
2.97-3.1310.0280.10721.6168249680668060.9970.113100
3.13-3.3210.0190.08925.2465056649364930.9980.094100
3.32-3.5510.0090.07130.4360976609260920.9980.074100
3.55-3.839.9780.05238.2656746568956870.9990.055100
3.83-4.29.9630.04244.4252513527552710.9990.04499.9
4.2-4.79.9110.03749.1647238477347660.9990.03999.9
4.7-5.429.8670.03946.4941738424542300.9990.04199.6
5.42-6.649.7520.04341.6535371364236270.9990.04599.6
6.64-9.399.570.03347.45270542858282710.03598.9
9.39-48.618.6930.02552.24141441702162710.02695.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3500)refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1vmd

1vmd


Resolution: 2.1→48.61 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.41
RfactorNum. reflection% reflectionSelection details
Rfree0.1841 2162 1.64 %0
Rwork0.1475 ---
obs0.1481 132058 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.16 Å2 / Biso mean: 28.5545 Å2 / Biso min: 7.73 Å2
Refinement stepCycle: final / Resolution: 2.1→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14161 0 76 1238 15475
Biso mean--24.01 38.3 -
Num. residues----1817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715180
X-RAY DIFFRACTIONf_angle_d0.87320784
X-RAY DIFFRACTIONf_dihedral_angle_d14.8229376
X-RAY DIFFRACTIONf_chiral_restr0.062356
X-RAY DIFFRACTIONf_plane_restr0.0052702
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6559X-RAY DIFFRACTION6.544TORSIONAL
12B6559X-RAY DIFFRACTION6.544TORSIONAL
13C6559X-RAY DIFFRACTION6.544TORSIONAL
14D6559X-RAY DIFFRACTION6.544TORSIONAL
15E6559X-RAY DIFFRACTION6.544TORSIONAL
16F6559X-RAY DIFFRACTION6.544TORSIONAL
17G6559X-RAY DIFFRACTION6.544TORSIONAL
18H6559X-RAY DIFFRACTION6.544TORSIONAL
19I6559X-RAY DIFFRACTION6.544TORSIONAL
110J6559X-RAY DIFFRACTION6.544TORSIONAL
111K6559X-RAY DIFFRACTION6.544TORSIONAL
112L6559X-RAY DIFFRACTION6.544TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.26721340.197485658699100
2.1489-2.20260.2591130.172585788691100
2.2026-2.26220.22881390.164585778716100
2.2622-2.32870.18891480.161785798727100
2.3287-2.40390.21191450.161985758720100
2.4039-2.48980.24321300.158886188748100
2.4898-2.58950.20821540.159985728726100
2.5895-2.70730.19071100.155586608770100
2.7073-2.85010.19541530.153286208773100
2.8501-3.02860.18131220.146286578779100
3.0286-3.26240.19081640.146686698833100
3.2624-3.59060.16961680.138686698837100
3.5906-4.10990.16031570.120187458902100
4.1099-5.17710.14121740.123687808954100
5.1771-48.62250.17981510.16099032918399
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.93320.7377-1.89692.6572-0.62514.9339-0.1212-0.0238-0.3688-0.0971-0.01880.42270.3156-0.36250.04820.1585-0.05630.0070.1680.05180.2346-24.271837.87571.9388
21.85390.7815-0.53923.0715-0.91562.8249-0.0730.1663-0.0798-0.19760.17750.31130.0471-0.3616-0.06790.0915-0.0032-0.00580.15310.04760.1936-22.846249.515967.3528
32.9186-0.8616-0.78651.7865-1.41643.7764-0.033-0.09410.30050.19740.20630.2113-0.27440.2198-0.2070.1161-0.02420.04160.1304-0.00140.1406-16.760250.415576.046
46.2329-4.59561.88598.6893-5.85084.9663-0.10740.33370.28980.064-0.0078-0.3496-0.4330.40640.05530.2736-0.03940.0040.1904-0.01360.1902-9.734839.742361.7719
51.74552.4675-0.46624.8809-1.36740.2058-0.15330.17990.0476-0.26780.1326-0.07010.0072-0.08590.04790.1581-0.01470.01110.12770.02840.1604-11.139945.285976.9007
64.52530.33-0.19032.89951.65335.4591-0.4443-0.3895-0.21850.3734-0.19540.5984-0.4788-0.4469-0.19560.27150.01160.07760.2060.03040.1923-21.512346.247589.4526
75.9765.2088-3.1374.9466-3.2732.04020.8181-1.00620.37351.0465-0.74160.1994-0.6720.61-0.19740.4148-0.07990.01290.2603-0.03870.2127-5.022558.439184.5296
86.75053.34181.11349.1309-3.21482.0770.2523-0.54240.5605-0.0025-0.5444-0.5875-0.49361.614-0.00250.2489-0.12150.02250.41450.02930.28129.002667.92574.4855
95.47081.63760.23572.8398-0.20612.05140.0179-0.0746-0.5606-0.2612-0.10480.14420.2250.0140.08760.19280.00240.00390.0878-0.01270.1757-7.51629.517984.3481
106.31922.9559-4.74373.1913-3.16664.15990.349-0.27520.38190.5363-0.101-0.0107-0.89950.1437-0.26790.2275-0.02320.00210.1326-0.02410.13661.530146.422889.7123
112.9590.7159-2.14493.0346-0.11545.9982-0.0536-0.1082-0.24460.2858-0.01790.21940.2763-0.36420.07370.1512-0.0079-0.00010.1610.04190.1087-3.183234.275693.0239
124.625-0.9044-3.59462.41561.51443.17260.0323-0.6854-0.10660.28430.0644-0.32380.06061.008-0.26030.1884-0.0215-0.00240.22730.00740.17198.340139.54592.4002
132.45140.4387-0.24322.2572.44023.1138-0.0762-0.0573-0.1-0.0030.0338-0.05850.21650.12610.02830.17210.03160.01060.10940.02970.14636.061231.714281.9585
143.3888-2.0288-0.95186.65892.37684.8374-0.27810.2063-0.3438-0.08380.06610.41160.5076-0.10040.1830.1858-0.0420.04360.11070.0130.1191-3.813931.930281.7283
152.6199-3.1466-1.69249.5342-2.47256.45230.0160.4041-0.3665-0.0733-0.0633-0.317-0.17660.27440.00340.2027-0.00720.02020.2185-0.01820.30065.255847.711375.5766
160.6723-0.9624-1.07945.64595.69945.75230.05420.07940.0344-0.26620.2813-0.3757-0.20760.3676-0.32780.2044-0.00540.00390.14540.00060.1963-5.414835.993574.3306
174.56791.7931-0.7675.1054-0.93661.36-0.02920.0432-0.35570.15310.05650.0350.1754-0.20390.00950.1554-0.02660.01810.16640.01250.1239-14.798935.0886.7985
184.4199-1.24731.51238.16634.65314.2746-0.31390.6324-0.1887-0.2162-0.16810.61710.7031-1.04470.46480.3025-0.1051-0.01730.2897-0.0790.2809-8.096223.144259.0202
194.6387-0.36460.76162.043-0.27572.7236-0.11960.0531-0.3063-0.14310.0732-0.12020.20450.20020.01910.2550.01680.05690.092-0.01220.152913.70521.716159.4117
201.8037-1.2418-1.66872.15091.32893.372-0.15960.0582-0.4026-0.1097-0.0560.02360.4535-0.12440.17540.26850.00370.06890.0817-0.01210.21417.393918.418262.9222
212.2139-1.61561.091.9099-1.62842.984-0.0527-0.08720.1703-0.14150.0274-0.04290.1681-0.28840.11840.22420.00830.01280.1646-0.0160.20597.71729.420360.5479
221.3279-0.4325-1.37293.29191.56325.05220.0008-0.0959-0.11920.1987-0.0128-0.05010.14540.02270.0290.17130.00330.04810.14360.00120.149619.873928.092662.7072
235.5361-1.7131-2.62564.00114.24354.8318-0.0914-0.27461.1580.27790.7379-1.20140.10961.0332-0.5730.25850.0278-0.02830.3623-0.08450.31917.724842.583782.3607
240.38990.90910.34574.19282.43044.897-0.03720.02190.0181-0.52020.0503-0.0983-0.0911-0.2215-0.00180.14620.03550.03150.21740.00560.174124.590335.740147.2016
255.5972-2.201-0.86783.47750.60774.0778-0.1242-0.1269-0.19190.13030.1357-0.18970.170.2720.00350.0793-0.02130.0310.1247-0.0180.185331.382840.329359.2057
261.7991-1.40521.53292.5205-0.55832.2631-0.03810.14660.2285-0.02440.0061-0.1408-0.10240.06130.00210.12990.01960.08840.15320.01630.172525.166746.590652.5503
275.7033-0.8596-3.0968.4977-2.5548.78670.0521-0.10270.1418-0.52620.02250.6264-0.35820.1335-0.0920.23760.0033-0.02850.1875-0.00160.19415.69546.658966.0255
283.9194-0.90791.83141.7817-1.09492.968-0.02170.1117-0.0846-0.15240.11340.0559-0.0653-0.0081-0.08680.1481-0.01370.03780.1080.00280.167320.343832.573552.2956
293.543-0.35894.76254.7107-1.94196.99061.01640.9852-1.1351-0.4104-0.75560.8390.6481-0.1031-0.19980.34990.0498-0.05850.2781-0.07530.33290.356137.284539.0688
303.38910.2084-0.59583.69010.21661.69450.0220.07650.2609-0.79080.0076-0.7649-0.24410.0422-0.16140.25750.04780.10170.1480.05670.22529.345163.846741.8484
312.1324-0.7853-0.09011.7713-1.21552.35180.34560.6491-0.2207-0.5461-0.27020.1699-0.2733-0.4734-0.10950.36820.1325-0.00970.3146-0.00810.1137-2.068355.012435.1869
323.3255-0.30340.42462.0236-0.39240.62750.1630.21310.0107-0.4555-0.2077-0.1262-0.1572-0.17380.08730.23570.06550.04940.1710.01780.11739.535850.06340.1647
334.98891.4715-2.62992.572-1.61322.50460.1120.0003-0.20480.1215-0.1552-0.07240.0201-0.03720.03490.23020.0181-0.00310.1786-0.00830.12911.840352.101447.2935
345.4467-1.59842.35570.6897-0.33871.46670.086-0.0068-0.2682-0.11860.0177-0.00450.07110.0134-0.12660.18930.02810.04270.14150.01750.13173.553660.409449.562
357.2483.4527-0.50815.73481.21173.99110.18720.3325-0.1026-0.7193-0.0169-0.9036-0.26680.2904-0.05840.30860.0370.11210.16380.05850.27097.030872.914342.5871
365.8959-5.53144.82915.5744-4.32674.1047-0.6085-0.1081.0840.6011-0.0542-0.474-0.70490.27140.76390.29570.0005-0.05730.26980.02220.444823.331559.262.8823
375.4914-0.9092.54960.1393-0.63594.51910.28030.0426-0.2011-0.1766-0.0601-0.00330.1427-0.4507-0.19420.17720.0104-0.0110.11120.02080.14-10.952568.945454.7685
383.6545-1.31970.49554.0762-1.47072.78820.03230.01710.3497-0.2226-0.104-0.2812-0.17880.24310.09920.1471-0.01350.02790.0634-0.01610.13660.921874.614761.0631
398.31575.9573-4.23625.1296-5.19447.3470.2227-0.75550.19961.0685-0.36-0.2271-0.53350.28530.11220.2043-0.0015-0.0270.1542-0.01150.1260.851274.965570.5352
402.43341.7760.21571.5391-0.33492.95730.0109-0.03240.1192-0.01960.00480.1563-0.0162-0.1074-0.03550.10470.00660.02760.07230.01080.1425-8.354766.163567.7815
412.27791.8936-2.79843.2186-1.25743.98030.17280.4256-0.0012-0.10930.08630.28810.1252-0.3632-0.29830.14720.01210.00660.08770.01450.1334-8.663666.092257.8626
429.8328-2.0099-2.51198.1682-2.78216.81240.0656-0.58560.0130.18470.03430.07680.5782-0.2102-0.10410.2203-0.02960.01240.2697-0.0170.22776.73757.753465.5994
434.36463.022-0.72983.31150.2410.52020.1682-0.3812-0.13270.1334-0.2404-0.07460.0380.02620.09430.19070.00610.03590.15710.02120.1385-3.586861.814154.1665
446.51960.1634-1.86855.328-3.12073.21760.04340.38980.2065-0.39970.07750.38360.0729-0.1944-0.14030.20460.0541-0.01840.16850.03270.0938-10.639971.575945.6503
456.68043.7426-1.0674.78880.0724.773-0.53740.51280.1695-0.93261.04661.16310.8148-0.3305-0.35550.3504-0.121-0.11260.32640.00590.2824-20.184945.17952.8124
461.6996-0.69160.03153.7871-2.11534.1106-0.0356-0.12880.04690.09220.02010.07940.01650.0004-0.05190.07560.0212-0.03230.1337-0.00770.163555.855445.06255.8084
474.1206-2.2395-1.8832.69010.9312.1904-0.03950.083-0.26810.04860.00310.31630.0691-0.1610.04940.092-0.0036-0.04090.1217-0.00780.170654.686437.772652.8206
482.6711-0.03741.40810.59310.61092.61910.0478-0.0263-0.08990.0516-0.1872-0.12110.54110.23160.15210.23940.0445-0.00740.14740.00350.207164.653940.951258.0104
493.2095-2.0584-1.62812.40850.94732.93740.09730.13190.2563-0.2393-0.0442-0.2480.01460.2029-0.03760.1439-0.0007-0.00590.13630.01990.18667.599750.287547.5142
503.85-0.0562-0.46252.62030.35083.2737-0.04210.19580.2324-0.07-0.09040.0058-0.2097-0.11290.09070.21280.0183-0.07510.08030.01090.119969.489162.380957.8062
512.8285-0.85861.61863.0248-1.32583.8494-0.16260.08590.3825-0.08070.0024-0.069-0.27380.21320.14960.2148-0.0209-0.06650.09430.01670.194375.779766.003361.3302
523.1422-1.562-0.68083.45682.13076.4158-0.1331-0.1598-0.2927-0.06040.0165-0.14780.15550.68370.13830.22040.0014-0.00820.15450.05440.202675.58354.852358.9484
531.6085-0.1752.03493.4402-2.31444.64890.0499-0.13660.06670.2056-0.0492-0.0247-0.0956-0.0762-0.00110.13720.0094-0.01880.1058-0.01050.133163.419455.813862.1428
544.36483.00220.71455.5801-3.17614.0399-0.3417-0.5783-0.83210.70290.76560.4526-0.1498-0.9699-0.37710.41370.05090.06360.40290.07290.318967.78641.327482.0904
554.90951.2357-1.13124.2742-0.32951.66740.06380.04260.73180.00050.0845-0.1104-0.10670.128-0.11730.18940.0179-0.04730.16720.00730.167192.882655.871681.5961
565.90711.69124.16713.96612.86044.3180.2351-0.1807-0.3340.56410.0482-0.07310.67670.1853-0.2920.25870.0029-0.0220.1950.02090.121485.763240.563689.3696
572.8381-0.51210.89681.3651-0.82433.4451-0.0578-0.0170.06010.06840.04360.0319-0.2414-0.05760.01940.17810.0074-0.03430.1054-0.02160.105481.579251.406683.7004
588.5782-3.50291.62464.89881.80767.540.05650.36540.1042-0.2310.09050.58270.1674-0.4275-0.120.2898-0.0161-0.01070.25370.00830.322279.178836.901974.0515
590.6247-1.2716-0.12064.6097-3.2713.6590.0573-0.00130.0438-0.21870.30560.34530.0751-0.3437-0.32670.1563-0.0018-0.05140.16270.00730.171891.55946.981575.4628
606.27530.1265-0.73386.1504-2.64812.28950.18960.31480.775-0.23230.08360.1105-0.01060.1639-0.30940.2481-0.0771-0.06070.2038-0.00410.288101.16255.093482.0713
614.59750.0004-0.80822.6224-2.39594.6979-0.57450.9370.0625-0.452-0.1693-0.6615-0.46141.69861.04570.393-0.11690.00760.4990.09950.398190.707761.813155.7656
622.3186-0.36170.0732.744-0.06824.0636-0.0405-0.11140.09070.11580.0886-0.3326-0.06620.446-0.03380.0782-0.0092-0.03850.215-0.02970.2622106.801840.480672.0597
632.15910.13310.96882.47351.89622.3955-0.07880.14290.0612-0.09340.2646-0.4210.04850.4098-0.04960.08250.00190.00170.2137-0.02460.2295104.965835.036765.4542
642.7332-4.7546-2.66348.9465.18633.1733-0.0030.7344-0.0439-0.4991-0.33750.14650.4688-0.40.28940.323-0.0667-0.02470.36390.02210.320693.43545.16559.125
654.02173.08210.50766.08921.36331.5943-0.0133-0.0261-0.13810.17840.0324-0.1430.15420.1514-0.01090.14490.0209-0.01990.1475-0.03270.164598.109838.613878.0476
664.65924.77054.44745.22055.01075.35310.551-1.0008-0.13980.9285-0.54150.03210.0832-0.9912-0.05420.448-0.109-0.01960.3260.01440.241681.445320.691177.1166
673.504-0.2253-1.80481.6441-0.35844.561-0.024-0.01220.1745-0.05940.1218-0.19690.26390.6736-0.04220.13010.0338-0.01590.1762-0.02460.159894.770115.611352.2994
684.7092-3.3415-2.5928.64865.75124.12260.0296-0.0106-0.38290.1672-0.2720.72830.151-0.41070.28080.16970.01560.00410.14310.00040.194377.25212.3461.8335
696.42850.082-0.36725.02330.14651.5886-0.01620.312-0.3423-0.35650.0473-0.06110.19020.1791-0.03570.21720.04110.0040.08220.00960.109789.5747.575657.3097
704.66194.72213.32225.66935.32866.82820.1486-0.5828-0.34610.8077-0.3336-0.02080.7950.09410.12840.25520.02970.00920.13680.01970.187883.9729.346569.1478
712.25061.71810.69212.92840.51663.1961-0.00760.0319-0.04480.1273-0.02-0.16610.02760.23250.05530.10110.05180.00220.1057-0.01370.135892.387918.542462.1705
728.5589-1.785.67842.78222.36859.6632-0.1475-0.49350.28410.2812-0.0073-0.0189-0.59330.47760.08620.29110.0030.00340.33530.06120.247876.387926.20964.3937
733.08221.26941.16414.10830.88171.60850.0346-0.03160.1358-0.0872-0.0659-0.07730.01090.21250.02960.14780.0364-0.00360.13970.020.088689.361519.502149.2895
748.86184.50882.06863.61060.79393.185-0.19090.5928-0.2596-1.52530.6154-1.5159-1.0462-0.0981-0.41120.4966-0.0920.14620.40550.01130.3156103.888140.265450.2052
753.3954-0.15020.26712.8506-0.38092.4360.17330.251-0.1198-0.3364-0.11930.11010.26520.1211-0.01890.21080.0809-0.01840.1712-0.03890.1280.198224.084637.1185
765.4968-3.238-3.09193.79462.60594.10150.48060.63940.4073-0.7341-0.2798-0.2228-0.22230.0292-0.19320.31290.09090.02550.23950.03930.183478.992335.350532.4988
776.6893-2.81310.28874.3291.46823.25770.07310.026-0.11720.0361-0.11220.3282-0.017-0.16550.06590.16250.0196-0.02040.1457-0.0160.130572.430627.94542.9924
782.5182-2.87633.03659.86610.12965.9041-0.06910.48790.42360.33280.24050.3557-0.4515-0.0104-0.12550.28470.01320.00840.29830.05550.346186.511438.362448.3817
794.1586-1.1897-1.38711.1637-0.14421.72520.0452-0.01620.0924-0.22040.00990.15040.0148-0.0079-0.07340.19050.0541-0.02660.1439-0.00680.138679.082320.903345.8863
804.5314-6.0393-1.04138.21212.21782.7574-0.746-0.0693-0.80221.02220.01821.06771.0088-0.22070.88840.2079-0.06350.09330.2108-0.00240.468165.679317.953354.5716
813.8422-4.2058-2.08867.1248-0.99845.4827-0.3047-0.9433-0.20921.83450.03850.8118-0.2985-0.27770.09680.44360.02090.13670.2909-0.01170.341357.117429.947767.8427
822.7044-0.62410.05214.02451.04885.776-0.0963-0.22720.26390.33520.1265-0.069-0.4886-0.2611-0.01750.18350.00970.04560.09230.04520.2048-18.24351.358680.7509
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 19 through 38 )G19 - 38
2X-RAY DIFFRACTION2chain 'G' and (resid 39 through 78 )G39 - 78
3X-RAY DIFFRACTION3chain 'G' and (resid 79 through 88 )G79 - 88
4X-RAY DIFFRACTION4chain 'G' and (resid 89 through 100 )G89 - 100
5X-RAY DIFFRACTION5chain 'G' and (resid 101 through 127 )G101 - 127
6X-RAY DIFFRACTION6chain 'G' and (resid 128 through 134 )G128 - 134
7X-RAY DIFFRACTION7chain 'G' and (resid 135 through 146 )G135 - 146
8X-RAY DIFFRACTION8chain 'G' and (resid 147 through 153 )G147 - 153
9X-RAY DIFFRACTION9chain 'H' and (resid 3 through 18 )H3 - 18
10X-RAY DIFFRACTION10chain 'H' and (resid 19 through 31 )H19 - 31
11X-RAY DIFFRACTION11chain 'H' and (resid 32 through 44 )H32 - 44
12X-RAY DIFFRACTION12chain 'H' and (resid 45 through 55 )H45 - 55
13X-RAY DIFFRACTION13chain 'H' and (resid 56 through 78 )H56 - 78
14X-RAY DIFFRACTION14chain 'H' and (resid 79 through 88 )H79 - 88
15X-RAY DIFFRACTION15chain 'H' and (resid 89 through 100 )H89 - 100
16X-RAY DIFFRACTION16chain 'H' and (resid 101 through 118 )H101 - 118
17X-RAY DIFFRACTION17chain 'H' and (resid 119 through 138 )H119 - 138
18X-RAY DIFFRACTION18chain 'H' and (resid 139 through 153 )H139 - 153
19X-RAY DIFFRACTION19chain 'I' and (resid 3 through 31 )I3 - 31
20X-RAY DIFFRACTION20chain 'I' and (resid 32 through 78 )I32 - 78
21X-RAY DIFFRACTION21chain 'I' and (resid 79 through 100 )I79 - 100
22X-RAY DIFFRACTION22chain 'I' and (resid 101 through 138 )I101 - 138
23X-RAY DIFFRACTION23chain 'I' and (resid 139 through 153 )I139 - 153
24X-RAY DIFFRACTION24chain 'J' and (resid 3 through 18 )J3 - 18
25X-RAY DIFFRACTION25chain 'J' and (resid 19 through 44 )J19 - 44
26X-RAY DIFFRACTION26chain 'J' and (resid 45 through 88 )J45 - 88
27X-RAY DIFFRACTION27chain 'J' and (resid 89 through 100 )J89 - 100
28X-RAY DIFFRACTION28chain 'J' and (resid 101 through 138 )J101 - 138
29X-RAY DIFFRACTION29chain 'J' and (resid 139 through 153 )J139 - 153
30X-RAY DIFFRACTION30chain 'K' and (resid 3 through 18 )K3 - 18
31X-RAY DIFFRACTION31chain 'K' and (resid 19 through 55 )K19 - 55
32X-RAY DIFFRACTION32chain 'K' and (resid 56 through 78 )K56 - 78
33X-RAY DIFFRACTION33chain 'K' and (resid 79 through 100 )K79 - 100
34X-RAY DIFFRACTION34chain 'K' and (resid 101 through 127 )K101 - 127
35X-RAY DIFFRACTION35chain 'K' and (resid 128 through 138 )K128 - 138
36X-RAY DIFFRACTION36chain 'K' and (resid 139 through 153 )K139 - 153
37X-RAY DIFFRACTION37chain 'L' and (resid 3 through 18 )L3 - 18
38X-RAY DIFFRACTION38chain 'L' and (resid 19 through 44 )L19 - 44
39X-RAY DIFFRACTION39chain 'L' and (resid 45 through 55 )L45 - 55
40X-RAY DIFFRACTION40chain 'L' and (resid 56 through 78 )L56 - 78
41X-RAY DIFFRACTION41chain 'L' and (resid 79 through 88 )L79 - 88
42X-RAY DIFFRACTION42chain 'L' and (resid 89 through 100 )L89 - 100
43X-RAY DIFFRACTION43chain 'L' and (resid 101 through 126 )L101 - 126
44X-RAY DIFFRACTION44chain 'L' and (resid 127 through 138 )L127 - 138
45X-RAY DIFFRACTION45chain 'L' and (resid 139 through 153 )L139 - 153
46X-RAY DIFFRACTION46chain 'A' and (resid 3 through 31 )A3 - 31
47X-RAY DIFFRACTION47chain 'A' and (resid 32 through 78 )A32 - 78
48X-RAY DIFFRACTION48chain 'A' and (resid 79 through 100 )A79 - 100
49X-RAY DIFFRACTION49chain 'A' and (resid 101 through 153 )A101 - 153
50X-RAY DIFFRACTION50chain 'B' and (resid 2 through 31 )B2 - 31
51X-RAY DIFFRACTION51chain 'B' and (resid 32 through 78 )B32 - 78
52X-RAY DIFFRACTION52chain 'B' and (resid 79 through 100 )B79 - 100
53X-RAY DIFFRACTION53chain 'B' and (resid 101 through 139 )B101 - 139
54X-RAY DIFFRACTION54chain 'B' and (resid 140 through 153 )B140 - 153
55X-RAY DIFFRACTION55chain 'C' and (resid 2 through 18 )C2 - 18
56X-RAY DIFFRACTION56chain 'C' and (resid 19 through 36 )C19 - 36
57X-RAY DIFFRACTION57chain 'C' and (resid 37 through 88 )C37 - 88
58X-RAY DIFFRACTION58chain 'C' and (resid 89 through 100 )C89 - 100
59X-RAY DIFFRACTION59chain 'C' and (resid 101 through 126 )C101 - 126
60X-RAY DIFFRACTION60chain 'C' and (resid 127 through 139 )C127 - 139
61X-RAY DIFFRACTION61chain 'C' and (resid 140 through 153 )C140 - 153
62X-RAY DIFFRACTION62chain 'D' and (resid 3 through 44 )D3 - 44
63X-RAY DIFFRACTION63chain 'D' and (resid 45 through 88 )D45 - 88
64X-RAY DIFFRACTION64chain 'D' and (resid 89 through 100 )D89 - 100
65X-RAY DIFFRACTION65chain 'D' and (resid 101 through 138 )D101 - 138
66X-RAY DIFFRACTION66chain 'D' and (resid 139 through 153 )D139 - 153
67X-RAY DIFFRACTION67chain 'E' and (resid 2 through 18 )E2 - 18
68X-RAY DIFFRACTION68chain 'E' and (resid 19 through 31 )E19 - 31
69X-RAY DIFFRACTION69chain 'E' and (resid 32 through 44 )E32 - 44
70X-RAY DIFFRACTION70chain 'E' and (resid 45 through 55 )E45 - 55
71X-RAY DIFFRACTION71chain 'E' and (resid 56 through 88 )E56 - 88
72X-RAY DIFFRACTION72chain 'E' and (resid 89 through 100 )E89 - 100
73X-RAY DIFFRACTION73chain 'E' and (resid 101 through 139 )E101 - 139
74X-RAY DIFFRACTION74chain 'E' and (resid 140 through 153 )E140 - 153
75X-RAY DIFFRACTION75chain 'F' and (resid 2 through 44 )F2 - 44
76X-RAY DIFFRACTION76chain 'F' and (resid 45 through 68 )F45 - 68
77X-RAY DIFFRACTION77chain 'F' and (resid 69 through 88 )F69 - 88
78X-RAY DIFFRACTION78chain 'F' and (resid 89 through 100 )F89 - 100
79X-RAY DIFFRACTION79chain 'F' and (resid 101 through 134 )F101 - 134
80X-RAY DIFFRACTION80chain 'F' and (resid 135 through 146 )F135 - 146
81X-RAY DIFFRACTION81chain 'F' and (resid 147 through 153 )F147 - 153
82X-RAY DIFFRACTION82chain 'G' and (resid 2 through 18 )G2 - 18

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

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Yorodumi

Thousand views of thousand structures

  • 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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