[English] 日本語
Yorodumi
- PDB-2xmz: Structure of MenH from S. aureus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xmz
TitleStructure of MenH from S. aureus
ComponentsHYDROLASE, ALPHA/BETA HYDROLASE FOLD FAMILY
KeywordsLYASE / MENAQUINONE BIOSYNTHESIS
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 / hydrolase activity
Similarity search - Function
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / Alpha/beta hydrolase family / alpha/beta hydrolase fold / 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
Putative 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / Putative 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsDawson, A. / Fyfe, P.K. / Gillet, F. / Hunter, W.N.
CitationJournal: Bmc Struct.Biol. / Year: 2011
Title: Exploiting the High-Resolution Crystal Structure of Staphylococcus Aureus Menh to Gain Insight Into Enzyme Activity.
Authors: Dawson, A. / Fyfe, P.K. / Gillet, F. / Hunter, W.N.
History
DepositionJul 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYDROLASE, ALPHA/BETA HYDROLASE FOLD FAMILY


Theoretical massNumber of molelcules
Total (without water)31,0191
Polymers31,0191
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.548, 43.563, 71.650
Angle α, β, γ (deg.)90.00, 98.26, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein HYDROLASE, ALPHA/BETA HYDROLASE FOLD FAMILY / 2-SUCCINYL-6-HYDROXY-2 / 4-CYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE


Mass: 31019.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: COL / Plasmid: PET15BTEV_SAMENH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5HH39, UniProt: A0A0H2WW38*PLUS, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUAL GH FROM TAG CLEAVAGE AT N-TERMINUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.5 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN BUFFER: 20 MM TRIS-HCL, 50 MM NACL, PH 7.5. RESERVOIR: 0.1 M NA HEPES PH 7.5, 25 % W/V PEG 4000.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 10, 2008 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→19.73 Å / Num. obs: 17242 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.5
Reflection shellResolution: 1.94→2.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R3D

1r3d


Resolution: 1.94→19.73 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.466 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24073 864 5 %RANDOM
Rwork0.18341 ---
obs0.18642 16378 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.652 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.23 Å2
2---0.74 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.94→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 0 185 2347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222259
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9563052
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2995265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48525.294119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32515428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5771510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211703
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6061.51329
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09222169
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7173930
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7364.5883
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.943→1.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 61 -
Rwork0.286 1046 -
obs--86.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.60830.2532-0.31624.6294-1.54544.30310.0135-0.06720.3198-0.10680.0346-0.349-0.37920.256-0.04810.1377-0.01910.05050.0223-0.02210.109112.27326.95616.493
21.7514-0.19570.04571.87580.31413.2264-0.00610.07070.0872-0.1226-0.04270.1223-0.2166-0.26170.04870.10150.0210.00850.0322-0.00150.01872.06317.17915.372
32.0897-0.5569-0.34511.73640.37712.5342-0.0212-0.1284-0.02750.07910.1824-0.17960.17170.2524-0.16120.09910.02810.00390.0395-0.02520.034612.9518.99920.564
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 45
2X-RAY DIFFRACTION2A46 - 119
3X-RAY DIFFRACTION3A120 - 265

+
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