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- PDB-7cj8: Crystal structure of N-terminal His-tagged D-allulose 3-epimerase... -

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Basic information

Entry
Database: PDB / ID: 7cj8
TitleCrystal structure of N-terminal His-tagged D-allulose 3-epimerase from Methylomonas sp. in complex with D-allulose
ComponentsEpimerase
KeywordsISOMERASE / Epimerase / TIM barrel
Function / homology
Function and homology information


D-tagatose 3-epimerase / isomerase activity / metal ion binding
Similarity search - Function
: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / D-psicose / L-ribulose 3-epimerase
Similarity search - Component
Biological speciesMethylomonas sp. DH-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsYoshida, H. / Yoshihara, A. / Kamitori, S.
CitationJournal: Febs Open Bio / Year: 2021
Title: Crystal structure of a novel homodimeric l-ribulose 3-epimerase from Methylomonus sp.
Authors: Yoshida, H. / Yoshihara, A. / Kato, S. / Mochizuki, S. / Akimitsu, K. / Izumori, K. / Kamitori, S.
History
DepositionJul 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epimerase
B: Epimerase
C: Epimerase
D: Epimerase
E: Epimerase
F: Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,39724
Polymers201,5566
Non-polymers2,84018
Water16,916939
1
A: Epimerase
B: Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1328
Polymers67,1852
Non-polymers9476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Epimerase
D: Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1328
Polymers67,1852
Non-polymers9476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Epimerase
F: Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1328
Polymers67,1852
Non-polymers9476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.020, 81.050, 106.130
Angle α, β, γ (deg.)99.300, 101.500, 87.240
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 1

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA0 - 28621 - 307
21TYRTYRBB0 - 28621 - 307
12TYRTYRAA0 - 28621 - 307
22TYRTYRCC0 - 28621 - 307
13ARGARGAA0 - 28521 - 306
23ARGARGDD0 - 28521 - 306
14TYRTYRAA0 - 28621 - 307
24TYRTYREE0 - 28621 - 307
15TYRTYRAA0 - 28621 - 307
25TYRTYRFF0 - 28621 - 307
16TYRTYRBB0 - 28621 - 307
26TYRTYRCC0 - 28621 - 307
17ARGARGBB0 - 28521 - 306
27ARGARGDD0 - 28521 - 306
18TYRTYRBB0 - 28621 - 307
28TYRTYREE0 - 28621 - 307
19TYRTYRBB0 - 28621 - 307
29TYRTYRFF0 - 28621 - 307
110ARGARGCC0 - 28521 - 306
210ARGARGDD0 - 28521 - 306
111TYRTYRCC0 - 28621 - 307
211TYRTYREE0 - 28621 - 307
112TYRTYRCC0 - 28621 - 307
212TYRTYRFF0 - 28621 - 307
113ARGARGDD0 - 28521 - 306
213ARGARGEE0 - 28521 - 306
114ARGARGDD0 - 28521 - 306
214ARGARGFF0 - 28521 - 306
115TYRTYREE0 - 28621 - 307
215TYRTYRFF0 - 28621 - 307

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.261342, -0.365362, 0.893427), (-0.340637, -0.900952, -0.268797), (0.903143, -0.234087, -0.359912)-17.77936, -23.882111, 15.16771
3given(1), (1), (1)
4given(0.233985, -0.34007, 0.910826), (-0.299671, -0.916446, -0.265185), (0.924905, -0.210898, -0.316344)-35.696739, -2.0106, 51.472172
5given(1), (1), (1)
6given(0.997415, 0.018469, 0.069438), (-0.018651, 0.999824, 0.001972), (-0.06939, -0.003262, 0.997584)19.68001, -21.923809, -35.803711
7given(1), (1), (1)
8given(0.101858, -0.293627, 0.950478), (-0.282334, -0.924692, -0.255405), (0.953893, -0.242337, -0.177088)10.50961, -60.805271, 28.301149
9given(1), (1), (1)
10given(0.986848, 0.059089, 0.150463), (-0.051373, 0.997182, -0.054665), (-0.153269, 0.046216, 0.987103)32.287369, 18.82519, 30.32482
11given(1), (1), (1)
12given(0.998548, 0.032881, 0.042676), (-0.03206, 0.99929, -0.019777), (-0.043296, 0.01838, 0.998893)20.654831, -21.66094, -34.95385
13given(1), (1), (1)
14given(0.204354, -0.338639, 0.918457), (-0.331318, -0.906809, -0.260627), (0.921123, -0.251042, -0.297507)-36.91333, -3.51926, 51.284458
15given(1), (1), (1)
16given(0.984297, 0.019347, 0.175459), (-0.006106, 0.997112, -0.075693), (-0.176417, 0.073433, 0.981573)31.8302, 19.857771, 30.47212
17given(1), (1), (1)
18given(0.136885, -0.282368, 0.94949), (-0.278513, -0.930818, -0.236662), (0.950628, -0.232049, -0.206058)12.22792, -60.316429, 27.79504
19given(1), (1), (1)
20given(0.174716, -0.29826, 0.938358), (-0.30746, -0.921888, -0.235778), (0.935384, -0.247314, -0.252771)-61.8009, 17.82242, 83.325684
21given(1), (1), (1)
22given(0.990705, -0.015729, 0.135114), (0.022919, 0.998393, -0.051822), (-0.134081, 0.054437, 0.989474)6.99973, 43.054852, 65.009064
23given(1), (1), (1)
24given(0.104592, -0.242201, 0.964572), (-0.256175, -0.943724, -0.209188), (0.960955, -0.22522, -0.160752)-9.89317, -37.75219, 63.085548
25given(1), (1), (1)
26given(0.040691, -0.258826, 0.965067), (-0.283505, -0.929161, -0.237242), (0.958107, -0.263947, -0.111187)-12.86948, -39.252899, 63.237572
27given(1), (1), (1)
28given(0.995898, 0.037131, 0.082514), (-0.032649, 0.997951, -0.055024), (-0.084388, 0.052105, 0.99507)7.22363, 40.7607, 66.925041
29given(1), (1), (1)
30given(-0.03123, -0.231328, 0.972374), (-0.205243, -0.950633, -0.232748), (0.978213, -0.206842, -0.01779)-18.331989, -80.518547, 0.00063

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Components

#1: Protein
Epimerase


Mass: 33592.691 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylomonas sp. DH-1 (bacteria) / Gene: AYM39_05640 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A172U6X0
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Sugar
ChemComp-PSJ / D-psicose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ethylene glycol, HEPES, PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→48.84 Å / Num. obs: 100753 / % possible obs: 97.6 % / Redundancy: 3.492 % / Biso Wilson estimate: 30.924 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.095 / Χ2: 0.931 / Net I/σ(I): 11.53 / Num. measured all: 351828 / Scaling rejects: 87
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
2.05-2.13.570.4962.7826210757873410.8350.58496.9
2.1-2.163.5170.3953.3525416746672260.8910.46896.8
2.16-2.223.3820.323.9623912728670710.9180.38297
2.22-2.293.4150.2874.423173697767860.9380.34297.3
2.29-2.373.5010.2595.0123144681266110.9480.30797
2.37-2.453.6120.2275.7723251661064380.9680.26697.4
2.45-2.543.5520.1956.522176638962430.9740.2397.7
2.54-2.653.4710.1617.4920644607259470.9810.19197.9
2.65-2.763.3330.138.6719137587457420.9860.15697.8
2.76-2.93.4490.1110.4918966562054990.990.13197.8
2.9-3.063.6060.08812.9318811531652170.9950.10398.1
3.06-3.243.5710.06915.8217753507049710.9960.08198
3.24-3.473.4390.0519.4715957472446400.9980.0698.2
3.47-3.743.3620.03923.4214633443643530.9980.04798.1
3.74-4.13.6450.03527.0814536406039880.9990.04198.2
4.1-4.583.5830.03129.1612827364935800.9990.03798.1
4.58-5.293.3040.03426.8710499324631780.9990.0497.9
5.29-6.483.5020.03924.19446273526970.9990.04698.6
6.48-9.173.540.0328.357387210920870.9990.03599
9.17-48.843.4710.02931.873950116411380.9990.03497.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZFS

5zfs


Resolution: 2.05→48.84 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.635 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 5031 5 %RANDOM
Rwork0.1618 ---
obs0.1658 95721 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.26 Å2 / Biso mean: 26.886 Å2 / Biso min: 14.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20.43 Å2-0.23 Å2
2--0.61 Å20.38 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.05→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13288 0 168 939 14395
Biso mean--38.86 35.29 -
Num. residues----1723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01313727
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712552
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.64318615
X-RAY DIFFRACTIONr_angle_other_deg1.1911.59429000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37451717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.44222.146727
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.388152161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5571590
X-RAY DIFFRACTIONr_chiral_restr0.0420.21765
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215583
X-RAY DIFFRACTIONr_gen_planes_other00.022991
X-RAY DIFFRACTIONr_rigid_bond_restr8.847326279
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2201TIGHT POSITIONAL0.260.11
1A2213TIGHT POSITIONAL0.360.11
1A2213TIGHT POSITIONAL0.410.11
1A2201TIGHT POSITIONAL0.370.11
1A2201TIGHT POSITIONAL0.390.11
1A2213TIGHT POSITIONAL0.310.11
1A2213TIGHT THERMAL7.971.12
2A2213TIGHT THERMAL7.81.12
3A2201TIGHT THERMAL5.471.12
4A2213TIGHT THERMAL8.351.12
5A2213TIGHT THERMAL5.111.12
6B2213TIGHT THERMAL5.81.12
7B2201TIGHT THERMAL8.191.12
8B2213TIGHT THERMAL5.71.12
9B2213TIGHT THERMAL8.91.12
10C2201TIGHT THERMAL7.061.12
11C2213TIGHT THERMAL6.131.12
12C2213TIGHT THERMAL8.841.12
13D2201TIGHT THERMAL8.821.12
14D2201TIGHT THERMAL5.561.12
15E2213TIGHT THERMAL9.591.12
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 398 -
Rwork0.196 6926 -
all-7324 -
obs--96.81 %

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