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- PDB-4i4z: Synechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A s... -

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Basic information

Entry
Database: PDB / ID: 4i4z
TitleSynechocystis sp. PCC 6803 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in complex with salicylyl-CoA
ComponentsNaphthoate synthase
KeywordsLYASE / crotonase / 1 / 4-dihydroxy-2-naphthoyl coenzyme A synthase
Function / homology
Function and homology information


phylloquinone biosynthetic process / 1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process / cytosol
Similarity search - Function
1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB / Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Salicylyl CoA / BICARBONATE ION / MALONATE ION / 1,4-dihydroxy-2-naphthoyl-CoA synthase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSong, H.G. / Sun, Y.R. / Li, J. / Li, Y. / Jiang, M. / Zhou, J.H. / Guo, Z.H.
CitationJournal: Plos One / Year: 2013
Title: Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme a synthase from the crotonase fold superfamily
Authors: Sun, Y. / Song, H. / Li, J. / Li, Y. / Jiang, M. / Zhou, J. / Guo, Z.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Naphthoate synthase
B: Naphthoate synthase
C: Naphthoate synthase
D: Naphthoate synthase
E: Naphthoate synthase
F: Naphthoate synthase
G: Naphthoate synthase
H: Naphthoate synthase
I: Naphthoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,83429
Polymers273,0929
Non-polymers8,74220
Water15,907883
1
A: Naphthoate synthase
B: Naphthoate synthase
C: Naphthoate synthase
D: Naphthoate synthase
E: Naphthoate synthase
F: Naphthoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,85519
Polymers182,0616
Non-polymers5,79413
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40950 Å2
ΔGint-189 kcal/mol
Surface area46410 Å2
MethodPISA
2
G: Naphthoate synthase
H: Naphthoate synthase
I: Naphthoate synthase
hetero molecules

G: Naphthoate synthase
H: Naphthoate synthase
I: Naphthoate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,95720
Polymers182,0616
Non-polymers5,89614
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area40400 Å2
ΔGint-184 kcal/mol
Surface area46190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.210, 139.210, 220.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11I-402-

HOH

21I-446-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19B
29C
110B
210D
111B
211E
112B
212F
113B
213G
114B
214H
115B
215I
116C
216D
117C
217E
118C
218F
119C
219G
120C
220H
121C
221I
122D
222E
123D
223F
124D
224G
125D
225H
126D
226I
127E
227F
128E
228G
129E
229H
130E
230I
131F
231G
132F
232H
133F
233I
134G
234H
135G
235I
136H
236I

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEUAA2 - 2742 - 274
21ASPASPLEULEUBB2 - 2742 - 274
12METMETPROPROAA1 - 2751 - 275
22METMETPROPROCC1 - 2751 - 275
13METMETPROPROAA1 - 2751 - 275
23METMETPROPRODD1 - 2751 - 275
14METMETPROPROAA1 - 2751 - 275
24METMETPROPROEE1 - 2751 - 275
15METMETPROPROAA1 - 2751 - 275
25METMETPROPROFF1 - 2751 - 275
16METMETPROPROAA1 - 2751 - 275
26METMETPROPROGG1 - 2751 - 275
17METMETPROPROAA1 - 2751 - 275
27METMETPROPROHH1 - 2751 - 275
18METMETPROPROAA1 - 2751 - 275
28METMETPROPROII1 - 2751 - 275
19ASPASPLEULEUBB2 - 2742 - 274
29ASPASPLEULEUCC2 - 2742 - 274
110ASPASPLEULEUBB2 - 2742 - 274
210ASPASPLEULEUDD2 - 2742 - 274
111ASPASPLEULEUBB2 - 2742 - 274
211ASPASPLEULEUEE2 - 2742 - 274
112ASPASPLEULEUBB2 - 2742 - 274
212ASPASPLEULEUFF2 - 2742 - 274
113ASPASPLEULEUBB2 - 2742 - 274
213ASPASPLEULEUGG2 - 2742 - 274
114ASPASPLEULEUBB2 - 2742 - 274
214ASPASPLEULEUHH2 - 2742 - 274
115ASPASPLEULEUBB2 - 2742 - 274
215ASPASPLEULEUII2 - 2742 - 274
116METMETPROPROCC1 - 2751 - 275
216METMETPROPRODD1 - 2751 - 275
117METMETPROPROCC1 - 2751 - 275
217METMETPROPROEE1 - 2751 - 275
118METMETPROPROCC1 - 2751 - 275
218METMETPROPROFF1 - 2751 - 275
119METMETPROPROCC1 - 2751 - 275
219METMETPROPROGG1 - 2751 - 275
120METMETPROPROCC1 - 2751 - 275
220METMETPROPROHH1 - 2751 - 275
121METMETPROPROCC1 - 2751 - 275
221METMETPROPROII1 - 2751 - 275
122METMETPROPRODD1 - 2751 - 275
222METMETPROPROEE1 - 2751 - 275
123METMETPROPRODD1 - 2751 - 275
223METMETPROPROFF1 - 2751 - 275
124METMETPROPRODD1 - 2751 - 275
224METMETPROPROGG1 - 2751 - 275
125METMETPROPRODD1 - 2751 - 275
225METMETPROPROHH1 - 2751 - 275
126METMETPROPRODD1 - 2751 - 275
226METMETPROPROII1 - 2751 - 275
127METMETPROPROEE1 - 2751 - 275
227METMETPROPROFF1 - 2751 - 275
128METMETPROPROEE1 - 2751 - 275
228METMETPROPROGG1 - 2751 - 275
129METMETPROPROEE1 - 2751 - 275
229METMETPROPROHH1 - 2751 - 275
130METMETPROPROEE1 - 2751 - 275
230METMETPROPROII1 - 2751 - 275
131METMETPROPROFF1 - 2751 - 275
231METMETPROPROGG1 - 2751 - 275
132METMETPROPROFF1 - 2751 - 275
232METMETPROPROHH1 - 2751 - 275
133METMETPROPROFF1 - 2751 - 275
233METMETPROPROII1 - 2751 - 275
134METMETPROPROGG1 - 2751 - 275
234METMETPROPROHH1 - 2751 - 275
135METMETPROPROGG1 - 2751 - 275
235METMETPROPROII1 - 2751 - 275
136METMETPROPROHH1 - 2751 - 275
236METMETPROPROII1 - 2751 - 275

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36

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Components

#1: Protein
Naphthoate synthase


Mass: 30343.508 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: menB, sll1127 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P73495, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Chemical
ChemComp-2NE / Salicylyl CoA


Mass: 887.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C28H40N7O18P3S
#3: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CHO3
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 883 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.15M ammonium acetate, 4% Tasmate, 0.1M Bis-tris, 15% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2011
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→44.67 Å / Num. all: 159143 / Num. obs: 158586 / % possible obs: 99.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.05 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EML

4eml


Resolution: 2→44.67 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.522 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22087 8387 5 %RANDOM
Rwork0.19847 ---
obs0.19959 158586 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.601 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.9 Å2-0 Å2
2--0.9 Å2-0 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19113 0 563 883 20559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01920133
X-RAY DIFFRACTIONr_bond_other_d0.0060.0218778
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.98727315
X-RAY DIFFRACTIONr_angle_other_deg1.087343089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2952470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53923.7908
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.737153177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.60315136
X-RAY DIFFRACTIONr_chiral_restr0.0710.22863
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02122971
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024744
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A163530.05
12B163530.05
21A165820.05
22C165820.05
31A162790.06
32D162790.06
41A164770.04
42E164770.04
51A163000.06
52F163000.06
61A163710.05
62G163710.05
71A161430.05
72H161430.05
81A163700.06
82I163700.06
91B163660.05
92C163660.05
101B161140.06
102D161140.06
111B162800.04
112E162800.04
121B161430.05
122F161430.05
131B162100.04
132G162100.04
141B159780.05
142H159780.05
151B162140.05
152I162140.05
161C163050.06
162D163050.06
171C165040.04
172E165040.04
181C163670.06
182F163670.06
191C164110.04
192G164110.04
201C161260.06
202H161260.06
211C164140.06
212I164140.06
221D162990.06
222E162990.06
231D163340.04
232F163340.04
241D161890.06
242G161890.06
251D160790.06
252H160790.06
261D163420.05
262I163420.05
271E162890.06
272F162890.06
281E163480.04
282G163480.04
291E161000.05
292H161000.05
301E163890.06
302I163890.06
311F161530.05
312G161530.05
321F160000.06
322H160000.06
331F163650.04
332I163650.04
341G160110.05
342H160110.05
351G162110.06
352I162110.06
361H161010.06
362I161010.06
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 586 -
Rwork0.261 11575 -
obs--99.05 %

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