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- PDB-5z2u: ThDP-Mn2+ complex of R395A variant of EcMenD soaked with 2-ketogl... -

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Basic information

Entry
Database: PDB / ID: 5z2u
TitleThDP-Mn2+ complex of R395A variant of EcMenD soaked with 2-ketoglutarate for 5 min
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / complex
Function / homology
Function and homology information


2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Menaquinone biosynthesis protein MenD, middle domain / Middle domain of thiamine pyrophosphate / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold ...Menaquinone biosynthesis protein MenD, middle domain / Middle domain of thiamine pyrophosphate / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-TD6 / THIAMINE DIPHOSPHATE / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsQin, M.M. / Guo, Z.H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Hong Kong
CitationJournal: Biochem. J. / Year: 2018
Title: Two active site arginines are critical determinants of substrate binding and catalysis in MenD: a thiamine-dependent enzyme in menaquinone biosynthesis.
Authors: Qin, M.M. / Song, H.G. / Dai, X. / Chen, Y.Z. / Guo, Z.H.
History
DepositionJan 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Aug 18, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)496,07640
Polymers490,7818
Non-polymers5,29432
Water59,1253282
1
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,96618
Polymers245,3914
Non-polymers2,57514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23160 Å2
ΔGint-109 kcal/mol
Surface area67720 Å2
MethodPISA
2
C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,11022
Polymers245,3914
Non-polymers2,71918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24580 Å2
ΔGint-112 kcal/mol
Surface area67570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.670, 90.700, 169.070
Angle α, β, γ (deg.)83.260, 75.960, 64.170
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...
21(CHAIN B AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...
31(CHAIN C AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...
41(CHAIN D AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...
51(CHAIN E AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...
61(CHAIN F AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...
71(CHAIN G AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...
81(CHAIN H AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN A AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...A0
211(CHAIN B AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...B0
311(CHAIN C AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...C0
411(CHAIN D AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...D0
511(CHAIN E AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...E0
611(CHAIN F AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...F0
711(CHAIN G AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...G0
811(CHAIN H AND (RESSEQ 2:5 OR (RESID 6 AND (NAME...H0

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / SEPHCHC synthase / Menaquinone biosynthesis protein MenD


Mass: 61347.664 Da / Num. of mol.: 8 / Mutation: R395A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: menD, b2264, JW5374 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

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Non-polymers , 7 types, 3314 molecules

#2: Chemical
ChemComp-TD6 / (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid


Mass: 527.403 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H25N4O10P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3282 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% v/v Jeffamine M-600 pH 7.0; 11.2% PEG 3350; 0.16M Mg formate; 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.35→37.27 Å / Num. obs: 177286 / % possible obs: 90.5 % / Redundancy: 2 % / CC1/2: 0.981 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.057 / Rrim(I) all: 0.081 / Net I/σ(I): 9.1 / Num. measured all: 346161
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2 % / Rmerge(I) obs: 0.085 / Num. measured all: 17574 / Num. unique obs: 8973 / CC1/2: 0.965 / Rpim(I) all: 0.085 / Rrim(I) all: 0.121 / Net I/σ(I) obs: 6.4 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
Aimlessdata scaling
PHENIXphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EJ8

5ej8


Resolution: 2.35→37.28 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 2.02 / Phase error: 17.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 1995 1.13 %
Rwork0.164 175283 -
obs0.165 177278 90.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.34 Å2 / Biso mean: 16.59 Å2 / Biso min: 1 Å2
Refinement stepCycle: final / Resolution: 2.35→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34202 0 339 3282 37823
Biso mean--15.03 22.94 -
Num. residues----4448
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A19631X-RAY DIFFRACTIONPOSITIONAL0
12B19631X-RAY DIFFRACTIONPOSITIONAL0
13C19631X-RAY DIFFRACTIONPOSITIONAL0
14D19631X-RAY DIFFRACTIONPOSITIONAL0
15E19631X-RAY DIFFRACTIONPOSITIONAL0
16F19631X-RAY DIFFRACTIONPOSITIONAL0
17G19631X-RAY DIFFRACTIONPOSITIONAL0
18H19631X-RAY DIFFRACTIONPOSITIONAL0
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 (%)
2.35-2.40880.26651360.188128061294292
2.4088-2.47390.24131550.1734127491290492
2.4739-2.54670.17351520.1637127421289492
2.5467-2.62880.24331320.1706127831291592
2.6288-2.72280.23681420.1749127101285292
2.7228-2.83170.23261480.1796128381298692
2.8317-2.96060.21911390.1695125651270491
2.9606-3.11660.19991450.1685126171276291
3.1166-3.31170.19181440.1665124661261091
3.3117-3.56730.2091440.1644124211256590
3.5673-3.92590.18631470.1546124771262490
3.9259-4.49310.18561320.1454117621189485
4.4931-5.65770.16621240.1508107791090378
5.6577-37.27920.16641550.164135681372398

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