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- PDB-7o74: Structure of cyanase from Pseudomonas lactis -

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Basic information

Entry
Database: PDB / ID: 7o74
TitleStructure of cyanase from Pseudomonas lactis
ComponentsCyanate hydratase
KeywordsLYASE / Hydrolase / Decamer / Nitrogen metabolism / Cyanate decomposition
Function / homology
Function and homology information


: / cyanase / cyanate hydratase activity / DNA binding
Similarity search - Function
: / Cyanate hydratase, N-terminal / Cyanate lyase, C-terminal / Cyanate hydratase / Cyanate lyase, C-terminal domain superfamily / Cyanate lyase C-terminal domain / Cyanate lyase C-terminal domain, Cyanate hydratase / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesPseudomonas lactis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsBrag, S. / Driller, J.H. / Pedersen, B.P.
CitationJournal: To Be Published
Title: Structure determination and analysis of unintentionally crystallized cyanase from Pseudomonas lactis
Authors: Brag, S. / Driller, J.H. / Pedersen, B.P.
History
DepositionApr 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Cyanate hydratase
B: Cyanate hydratase
C: Cyanate hydratase
D: Cyanate hydratase
E: Cyanate hydratase
F: Cyanate hydratase
G: Cyanate hydratase
H: Cyanate hydratase
I: Cyanate hydratase
J: Cyanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,70419
Polymers169,38510
Non-polymers3199
Water33,6341867
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area63830 Å2
ΔGint-510 kcal/mol
Surface area47380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.146, 117.592, 106.991
Angle α, β, γ (deg.)90.000, 94.260, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-342-

HOH

21A-402-

HOH

31A-507-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 16 or resid 18...
21(chain B and (resid 1 through 16 or resid 18...
31(chain C and (resid 1 through 16 or resid 18...
41(chain D and (resid 1 through 16 or resid 18...
51(chain E and (resid 1 through 16 or resid 18...
61(chain F and (resid 1 through 16 or resid 18...
71(chain G and (resid 1 through 16 or resid 18...
81(chain H and (resid 1 through 16 or resid 18...
91(chain I and (resid 1 through 16 or resid 18...
101(chain J and (resid 1 through 16 or resid 18...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 16 or resid 18...A1 - 16
121(chain A and (resid 1 through 16 or resid 18...A18 - 38
131(chain A and (resid 1 through 16 or resid 18...A40 - 55
141(chain A and (resid 1 through 16 or resid 18...A57 - 60
151(chain A and (resid 1 through 16 or resid 18...A70 - 74
161(chain A and (resid 1 through 16 or resid 18...A1 - 156
171(chain A and (resid 1 through 16 or resid 18...A87 - 85
181(chain A and (resid 1 through 16 or resid 18...A0
191(chain A and (resid 1 through 16 or resid 18...A1 - 156
1101(chain A and (resid 1 through 16 or resid 18...A32 - 13336
1111(chain A and (resid 1 through 16 or resid 18...A1 - 156
1121(chain A and (resid 1 through 16 or resid 18...A139
1131(chain A and (resid 1 through 16 or resid 18...A139
1141(chain A and (resid 1 through 16 or resid 18...A141 - 153
1151(chain A and (resid 1 through 16 or resid 18...A155 - 156
211(chain B and (resid 1 through 16 or resid 18...B1 - 16
221(chain B and (resid 1 through 16 or resid 18...B18 - 38
231(chain B and (resid 1 through 16 or resid 18...B40 - 55
241(chain B and (resid 1 through 16 or resid 18...B70 - 74
251(chain B and (resid 1 through 16 or resid 18...B1 - 68
261(chain B and (resid 1 through 16 or resid 18...B76
271(chain B and (resid 1 through 16 or resid 18...B78
281(chain B and (resid 1 through 16 or resid 18...B87 - 129
291(chain B and (resid 1 through 16 or resid 18...B13
2101(chain B and (resid 1 through 16 or resid 18...B135 - 136
2111(chain B and (resid 1 through 16 or resid 18...B139
2121(chain B and (resid 1 through 16 or resid 18...B141 - 153
2131(chain B and (resid 1 through 16 or resid 18...B155 - 156
311(chain C and (resid 1 through 16 or resid 18...C1 - 16
321(chain C and (resid 1 through 16 or resid 18...C18 - 38
331(chain C and (resid 1 through 16 or resid 18...C1 - 156
341(chain C and (resid 1 through 16 or resid 18...C0
351(chain C and (resid 1 through 16 or resid 18...C62 - 68
361(chain C and (resid 1 through 16 or resid 18...C70 - 74
371(chain C and (resid 1 through 16 or resid 18...C76
381(chain C and (resid 1 through 16 or resid 18...C78 - 85
391(chain C and (resid 1 through 16 or resid 18...C87 - 129
3101(chain C and (resid 1 through 16 or resid 18...C132 - 133
3111(chain C and (resid 1 through 16 or resid 18...C135 - 136
3121(chain C and (resid 1 through 16 or resid 18...C139
3131(chain C and (resid 1 through 16 or resid 18...C141 - 153
3141(chain C and (resid 1 through 16 or resid 18...C155 - 156
411(chain D and (resid 1 through 16 or resid 18...D1 - 16
421(chain D and (resid 1 through 16 or resid 18...D18 - 38
431(chain D and (resid 1 through 16 or resid 18...D40 - 55
441(chain D and (resid 1 through 16 or resid 18...D57 - 60
451(chain D and (resid 1 through 16 or resid 18...D62 - 68
461(chain D and (resid 1 through 16 or resid 18...D70 - 74
471(chain D and (resid 1 through 16 or resid 18...D76
481(chain D and (resid 1 through 16 or resid 18...D78 - 85
491(chain D and (resid 1 through 16 or resid 18...D87 - 129
4101(chain D and (resid 1 through 16 or resid 18...D132 - 133
4111(chain D and (resid 1 through 16 or resid 18...D135 - 136
4121(chain D and (resid 1 through 16 or resid 18...D139
4131(chain D and (resid 1 through 16 or resid 18...D141 - 153
4141(chain D and (resid 1 through 16 or resid 18...D155 - 156
511(chain E and (resid 1 through 16 or resid 18...E1 - 16
521(chain E and (resid 1 through 16 or resid 18...E18 - 38
531(chain E and (resid 1 through 16 or resid 18...E40 - 55
541(chain E and (resid 1 through 16 or resid 18...E57 - 60
551(chain E and (resid 1 through 16 or resid 18...E62 - 68
561(chain E and (resid 1 through 16 or resid 18...E70 - 74
571(chain E and (resid 1 through 16 or resid 18...E76
581(chain E and (resid 1 through 16 or resid 18...E78 - 85
591(chain E and (resid 1 through 16 or resid 18...E87 - 129
5101(chain E and (resid 1 through 16 or resid 18...E132 - 133
5111(chain E and (resid 1 through 16 or resid 18...E135 - 136
5121(chain E and (resid 1 through 16 or resid 18...E139
5131(chain E and (resid 1 through 16 or resid 18...E141 - 153
5141(chain E and (resid 1 through 16 or resid 18...E155 - 156
611(chain F and (resid 1 through 16 or resid 18...F1 - 16
621(chain F and (resid 1 through 16 or resid 18...F18 - 38
631(chain F and (resid 1 through 16 or resid 18...F40 - 55
641(chain F and (resid 1 through 16 or resid 18...F57 - 60
651(chain F and (resid 1 through 16 or resid 18...F62 - 68
661(chain F and (resid 1 through 16 or resid 18...F70 - 74
671(chain F and (resid 1 through 16 or resid 18...F76
681(chain F and (resid 1 through 16 or resid 18...F78 - 85
691(chain F and (resid 1 through 16 or resid 18...F87 - 129
6101(chain F and (resid 1 through 16 or resid 18...F132 - 133
6111(chain F and (resid 1 through 16 or resid 18...F135 - 136
6121(chain F and (resid 1 through 16 or resid 18...F139
6131(chain F and (resid 1 through 16 or resid 18...F141 - 153
6141(chain F and (resid 1 through 16 or resid 18...F155 - 156
711(chain G and (resid 1 through 16 or resid 18...G1 - 16
721(chain G and (resid 1 through 16 or resid 18...G18 - 38
731(chain G and (resid 1 through 16 or resid 18...G40 - 55
741(chain G and (resid 1 through 16 or resid 18...G62 - 68
751(chain G and (resid 1 through 16 or resid 18...G70 - 74
761(chain G and (resid 1 through 16 or resid 18...G76
771(chain G and (resid 1 through 16 or resid 18...G78 - 85
781(chain G and (resid 1 through 16 or resid 18...G87 - 129
791(chain G and (resid 1 through 16 or resid 18...G132 - 133
7101(chain G and (resid 1 through 16 or resid 18...G135 - 136
7111(chain G and (resid 1 through 16 or resid 18...G139
7121(chain G and (resid 1 through 16 or resid 18...G141 - 153
7131(chain G and (resid 1 through 16 or resid 18...G155 - 156
811(chain H and (resid 1 through 16 or resid 18...H1 - 16
821(chain H and (resid 1 through 16 or resid 18...H18 - 38
831(chain H and (resid 1 through 16 or resid 18...H40 - 55
841(chain H and (resid 1 through 16 or resid 18...H57 - 60
851(chain H and (resid 1 through 16 or resid 18...H62 - 68
861(chain H and (resid 1 through 16 or resid 18...H70 - 74
871(chain H and (resid 1 through 16 or resid 18...H76
881(chain H and (resid 1 through 16 or resid 18...H78 - 85
891(chain H and (resid 1 through 16 or resid 18...H87 - 129
8101(chain H and (resid 1 through 16 or resid 18...H132 - 133
8111(chain H and (resid 1 through 16 or resid 18...H135 - 136
8121(chain H and (resid 1 through 16 or resid 18...H139
8131(chain H and (resid 1 through 16 or resid 18...H141 - 153
8141(chain H and (resid 1 through 16 or resid 18...H155 - 156
911(chain I and (resid 1 through 16 or resid 18...I1 - 16
921(chain I and (resid 1 through 16 or resid 18...I18 - 38
931(chain I and (resid 1 through 16 or resid 18...I40 - 55
941(chain I and (resid 1 through 16 or resid 18...I57 - 60
951(chain I and (resid 1 through 16 or resid 18...I62 - 68
961(chain I and (resid 1 through 16 or resid 18...I70 - 74
971(chain I and (resid 1 through 16 or resid 18...I76
981(chain I and (resid 1 through 16 or resid 18...I78 - 85
991(chain I and (resid 1 through 16 or resid 18...I87 - 129
9101(chain I and (resid 1 through 16 or resid 18...I132 - 133
9111(chain I and (resid 1 through 16 or resid 18...I135 - 136
9121(chain I and (resid 1 through 16 or resid 18...I139
9131(chain I and (resid 1 through 16 or resid 18...I141 - 153
9141(chain I and (resid 1 through 16 or resid 18...I155 - 156
1011(chain J and (resid 1 through 16 or resid 18...J1 - 16
1021(chain J and (resid 1 through 16 or resid 18...J18 - 38
1031(chain J and (resid 1 through 16 or resid 18...J40 - 55
1041(chain J and (resid 1 through 16 or resid 18...J57 - 60
1051(chain J and (resid 1 through 16 or resid 18...J62 - 68
1061(chain J and (resid 1 through 16 or resid 18...J70 - 74
1071(chain J and (resid 1 through 16 or resid 18...J76
1081(chain J and (resid 1 through 16 or resid 18...J78 - 85
1091(chain J and (resid 1 through 16 or resid 18...J87 - 129
10101(chain J and (resid 1 through 16 or resid 18...J132 - 133
10111(chain J and (resid 1 through 16 or resid 18...J135 - 136
10121(chain J and (resid 1 through 16 or resid 18...J139
10131(chain J and (resid 1 through 16 or resid 18...J141 - 153
10141(chain J and (resid 1 through 16 or resid 18...J155 - 156

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Components

#1: Protein
Cyanate hydratase / Cyanase / Cyanate hydrolase / Cyanate lyase


Mass: 16938.469 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Pseudomonas lactis (bacteria) / References: UniProt: A0A218ZZ45, cyanase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1867 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MemGold B9 0.1M Potassium chloride 0.02M Tris7.0 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.61→43.57 Å / Num. obs: 202687 / % possible obs: 97.4 % / Redundancy: 6.944 % / Biso Wilson estimate: 20.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.169 / Rrim(I) all: 0.183 / Χ2: 0.812 / Net I/σ(I): 8.28 / Num. measured all: 1407503 / Scaling rejects: 81
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
1.61-1.656.7072.7061.049697415348144590.2412.93194.2
1.65-1.696.9842.1581.4110055014968143980.3432.33196.2
1.69-1.746.9251.8841.669711614534140230.4242.03696.5
1.74-1.86.8031.5482.099314614170136910.531.67796.6
1.8-1.867.0161.2422.779284913662132340.6961.34196.9
1.86-1.926.8670.9683.518850713283128880.7841.04897
1.92-1.997.0490.7344.528774312801124470.8710.79197.2
1.99-2.077.150.555.88569212294119850.9280.59397.5
2.07-2.177.1160.4177.058223411824115560.9560.4597.7
2.17-2.277.1190.3128.547863211299110460.9710.33797.8
2.27-2.47.1510.2519.857555210760105650.9790.2798.2
2.4-2.547.0990.19611.327105910187100100.9860.21298.3
2.54-2.727.0070.16412.665933955194090.9880.17898.5
2.72-2.937.0490.12515.0362030892088000.9920.13698.7
2.93-3.216.9250.117.4456184820681130.9940.10898.9
3.21-3.596.8760.07920.850487741773420.9950.08599
3.59-4.156.6680.06823.0343535658165290.9950.07499.2
4.15-5.086.4030.06223.8735398557155280.9960.06799.2
5.08-7.196.5470.06123.7528029431542810.9960.06699.2
7.19-43.576.6530.05526.115853240623830.9970.0699

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.22 Å46.54 Å

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
XDSFeb 5, 2021data reduction
XSCALEFeb 5, 2021data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4y42

4y42


Resolution: 1.61→43.57 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1898 2022 1 %
Rwork0.1639 200388 -
obs0.1641 202410 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.11 Å2 / Biso mean: 25.1156 Å2 / Biso min: 10.84 Å2
Refinement stepCycle: final / Resolution: 1.61→43.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11920 0 9 1867 13796
Biso mean--23.37 34.34 -
Num. residues----1560
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3880X-RAY DIFFRACTION1.145TORSIONAL
12B3880X-RAY DIFFRACTION1.145TORSIONAL
13C3880X-RAY DIFFRACTION1.145TORSIONAL
14D3880X-RAY DIFFRACTION1.145TORSIONAL
15E3880X-RAY DIFFRACTION1.145TORSIONAL
16F3880X-RAY DIFFRACTION1.145TORSIONAL
17G3880X-RAY DIFFRACTION1.145TORSIONAL
18H3880X-RAY DIFFRACTION1.145TORSIONAL
19I3880X-RAY DIFFRACTION1.145TORSIONAL
110J3880X-RAY DIFFRACTION1.145TORSIONAL
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 (%)
1.61-1.650.32441370.3135134241356192
1.65-1.690.30221400.2875141351427596
1.69-1.740.34371430.2684141181426196
1.74-1.80.27851430.2616142101435397
1.8-1.860.26881440.2285142471439197
1.86-1.940.23221430.1897142311437497
1.94-2.020.21631460.1742143051445197
2.02-2.130.1891440.1643143541449898
2.13-2.260.18571450.1557143951454098
2.26-2.440.19111490.1521144571460698
2.44-2.680.20191440.1577144691461398
2.68-3.070.18991470.1581145491469699
3.07-3.870.16471490.1396146591480899
3.87-43.570.13271480.1312148351498399

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