[English] 日本語
Yorodumi
- PDB-4eac: Crystal structure of mannonate dehydratase from Escherichia coli ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eac
TitleCrystal structure of mannonate dehydratase from Escherichia coli strain K12
ComponentsMannonate dehydratase
KeywordsLYASE / TIM Barrel / Dehydratase
Function / homology
Function and homology information


D-glucuronate catabolic process / mannonate dehydratase / mannonate dehydratase activity / ferrous iron binding / manganese ion binding / DNA damage response
Similarity search - Function
Mannonate dehydratase / D-mannonate dehydratase (UxuA) / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Mannonate dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsQiu, X. / Zhu, Y. / Yuan, Y. / Zhang, Y. / Liu, H. / Gao, Y. / Teng, M. / Niu, L.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structural insights into decreased enzymatic activity induced by an insert sequence in mannonate dehydratase from Gram negative bacterium.
Authors: Qiu, X. / Tao, Y. / Zhu, Y. / Yuan, Y. / Zhang, Y. / Liu, H. / Gao, Y. / Teng, M. / Niu, L.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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_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: Mannonate dehydratase
B: Mannonate dehydratase
C: Mannonate dehydratase
D: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,63912
Polymers188,2774
Non-polymers3628
Water16,015889
1
A: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1603
Polymers47,0691
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1603
Polymers47,0691
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1603
Polymers47,0691
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1603
Polymers47,0691
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.961, 238.461, 54.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: -1 - 393 / Label seq-ID: 19 - 413

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
Mannonate dehydratase / D-mannonate hydrolase


Mass: 47069.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: uxuA, b4322, JW4285 / Production host: Escherichia coli (E. coli) / References: UniProt: P24215, mannonate dehydratase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.1M Tris-HCl,0.1M magnesium chloride hexahydrate , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: MX-225 CCD / Detector: CCD / Date: Jun 23, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.3→132.27 Å / Num. all: 92475 / Num. obs: 92475 / % possible obs: 99.7 % / Observed criterion σ(F): 3.7 / Observed criterion σ(I): 3.7
Reflection shellResolution: 2.3→2.34 Å / % possible all: 95.7

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FVM

3fvm


Resolution: 2.3→48.42 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.188 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 3.7 / ESU R: 0.271 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21863 4630 5 %RANDOM
Rwork0.18291 ---
all0.1847 92475 --
obs0.1847 92475 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.102 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---1.36 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12594 0 8 889 13491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02212882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.94717467
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12751577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65423.841643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.446152191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.49615104
X-RAY DIFFRACTIONr_chiral_restr0.0790.21897
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219928
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_it0.4021.57877
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.777212713
X-RAY DIFFRACTIONr_scbond_it1.21735005
X-RAY DIFFRACTIONr_scangle_it2.064.54754
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3136 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.330.5
Bmedium positional0.250.5
Cmedium positional0.330.5
Dmedium positional0.280.5
Amedium thermal0.512
Bmedium thermal0.412
Cmedium thermal0.472
Dmedium thermal0.392
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 352 -
Rwork0.198 6306 -
obs--97.98 %
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)
10.49890.0377-0.01770.8337-0.23791.3525-0.00160.0106-0.0643-0.002-0.1085-0.1366-0.14170.23510.11010.034-0.0287-0.00560.08660.04250.0440.71211.030424.7356
20.502-0.1520.01451.6472-0.49431.054-0.0291-0.0452-0.012-0.07380.11310.152-0.1062-0.2251-0.0840.06160.0230.0080.08610.01950.018147.417543.47475.9021
30.9704-0.3236-0.4660.84210.18621.02830.1885-0.07350.3159-0.1662-0.0034-0.2402-0.3210.073-0.18510.1698-0.02660.08750.0294-0.01280.1515-8.107522.86787.4185
40.74680.5141-0.22131.1669-0.21140.7969-0.12860.0485-0.3392-0.16240.0805-0.62240.19490.24570.04810.1490.03070.0960.1578-0.06090.39617.757868.358231.6427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 393
2X-RAY DIFFRACTION2B-1 - 393
3X-RAY DIFFRACTION3C-1 - 394
4X-RAY DIFFRACTION4D-1 - 393

+
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