[English] 日本語
Yorodumi
- PDB-3hwx: Crystal structure of menaquinone synthesis protein MenD from E. c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hwx
TitleCrystal structure of menaquinone synthesis protein MenD from E. coli in complex with ThDP
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / menaquinone / ThDP / Mg / vitamin K2 / carboxylase / Magnesium / Manganese / Menaquinone biosynthesis / Metal-binding / Thiamine pyrophosphate
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
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: 2.6 Å
AuthorsPriyadarshi, A. / Hwang, K.Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structural and functional analysis of Vitamin K2 synthesis protein MenD.
Authors: Priyadarshi, A. / Kim, E.E. / Hwang, K.Y.
History
DepositionJun 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
I: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
J: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
R: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
S: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Z: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
1: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)495,72541
Polymers491,5998
Non-polymers4,12633
Water8,125451
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8689
Polymers122,9002
Non-polymers9687
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-42 kcal/mol
Surface area39080 Å2
MethodPISA
2
I: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
J: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,96010
Polymers122,9002
Non-polymers1,0608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-40 kcal/mol
Surface area39370 Å2
MethodPISA
3
R: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
S: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,93712
Polymers122,9002
Non-polymers1,03710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-43 kcal/mol
Surface area39190 Å2
MethodPISA
4
Z: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
1: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,96010
Polymers122,9002
Non-polymers1,0608
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-43 kcal/mol
Surface area39550 Å2
MethodPISA
5
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
I: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
J: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,82819
Polymers245,7994
Non-polymers2,02915
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21220 Å2
ΔGint-94 kcal/mol
Surface area70980 Å2
MethodPISA
6
R: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
S: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Z: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
1: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,89722
Polymers245,7994
Non-polymers2,09718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21440 Å2
ΔGint-100 kcal/mol
Surface area71120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.353, 90.463, 169.170
Angle α, β, γ (deg.)75.99, 83.00, 64.15
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 8 molecules ABIJRSZ1

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


Mass: 61449.828 Da / Num. of mol.: 8 / Mutation: P36L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2264, JW5374, menD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

-
Non-polymers , 5 types, 484 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 8K, 10% glycerol, 1mM ThDP, 5mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 13, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 141599 / Num. obs: 114098 / % possible obs: 83.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.26 / Net I/σ(I): 6.22
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4413 / Rsym value: 0.26 / % possible all: 48.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JLC

2jlc


Resolution: 2.6→47.69 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.835 / SU B: 11.452 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25271 5978 5 %RANDOM
Rwork0.19667 ---
obs0.19946 114098 83.51 %-
all-141599 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20.04 Å2-0.02 Å2
2---0.02 Å2-0.01 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34608 0 243 451 35302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02135686
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.95448695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89554429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25923.631620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.38155664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.99415280
X-RAY DIFFRACTIONr_chiral_restr0.1140.25396
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02127428
X-RAY DIFFRACTIONr_mcbond_it0.591.522140
X-RAY DIFFRACTIONr_mcangle_it1.108235533
X-RAY DIFFRACTIONr_scbond_it1.868313546
X-RAY DIFFRACTIONr_scangle_it3.0554.513162
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 354 -
Rwork0.241 7033 -
obs-6000 69.35 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more