[English] 日本語
Yorodumi
- PDB-4gdm: Crystal Structure of E.coli MenH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gdm
TitleCrystal Structure of E.coli MenH
Components2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
KeywordsLYASE / menaquinone biosynthesis / alpha beta hydrolase / 2-succinyl-6-hydroxy-2 / 4-cyclohexadiene-1-carboxylate synthase / MenH
Function / homology
Function and homology information


2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase activity / menaquinone biosynthetic process / cytosol
Similarity search - Function
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsJohnston, J.M. / Baker, E.N. / Guo, Z. / Jiang, M.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structures of E. coli Native MenH and Two Active Site Mutants.
Authors: Johnston, J.M. / Jiang, M. / Guo, Z. / Baker, E.N.
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Feb 4, 2015Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
B: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
C: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,12911
Polymers88,5463
Non-polymers5838
Water1,17165
1
A: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6473
Polymers29,5151
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8355
Polymers29,5151
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6473
Polymers29,5151
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.664, 116.664, 476.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / / SHCHC synthase


Mass: 29515.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2263, JW2258, menH, yfbB / Plasmid: pETM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P37355, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 4.58 Å3/Da / Density % sol: 73.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Sodium Citrate, Ammonium sulfate, Lithium sulfate, pH 5.5, vapor diffusion, hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.75→45.774 Å / Num. all: 43461 / Num. obs: 43437 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 17.5 % / Biso Wilson estimate: 69.92 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 22.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4266

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→45.77 Å / Cor.coef. Fo:Fc: 0.9414 / Cor.coef. Fo:Fc free: 0.9149 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.291 / SU Rfree Blow DPI: 0.225 / SU Rfree Cruickshank DPI: 0.228 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2182 5.02 %RANDOM
Rwork0.1919 ---
obs0.1935 43432 99.94 %-
Displacement parametersBiso max: 135.83 Å2 / Biso mean: 53.7247 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--2.0462 Å20 Å20 Å2
2---2.0462 Å20 Å2
3---4.0924 Å2
Refine analyzeLuzzati coordinate error obs: 0.367 Å
Refinement stepCycle: LAST / Resolution: 2.75→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5949 0 29 65 6043
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2753SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC2
X-RAY DIFFRACTIONt_gen_planes921HARMONIC5
X-RAY DIFFRACTIONt_it6110HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion743SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6877SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6110HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8297HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion3.19
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3022 153 4.92 %
Rwork0.2726 2954 -
all0.2742 3107 -
obs--99.94 %

+
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