[English] 日本語
Yorodumi
- PDB-4n81: Another flexible region at the active site of an inositol monopho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n81
TitleAnother flexible region at the active site of an inositol monophosphatase from Zymomonas mobilis
ComponentsInositol monophosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


phosphoric ester hydrolase activity / metal ion binding
Similarity search - Function
: / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Inositol monophosphatase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsHwang, H.J. / Park, S.Y. / Kim, J.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure of cbbF from Zymomonas mobilis and its functional implication
Authors: Hwang, H.J. / Park, S.Y. / Kim, J.S.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7752
Polymers28,6791
Non-polymers961
Water5,260292
1
A: Inositol monophosphatase
hetero molecules

A: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5494
Polymers57,3572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3530 Å2
ΔGint-32 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.747, 90.747, 75.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

-
Components

#1: Protein Inositol monophosphatase / IMPase/FBPase


Mass: 28678.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Strain: ZM4 / Gene: ZMO1518 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NMB8, inositol-phosphate phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 11%(w/v) polyethylene glycol 4000, 0.2M Lithium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 28603 / Num. obs: 28603 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.22 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→39.295 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9026 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 16.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 2832 9.91 %RANDOM
Rwork0.1458 ---
all0.1491 28577 --
obs0.1491 28577 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.7 Å2 / Biso mean: 24.4505 Å2 / Biso min: 7.48 Å2
Refinement stepCycle: LAST / Resolution: 1.901→39.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 5 292 2270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192032
X-RAY DIFFRACTIONf_angle_d1.7212757
X-RAY DIFFRACTIONf_chiral_restr0.15302
X-RAY DIFFRACTIONf_plane_restr0.011365
X-RAY DIFFRACTIONf_dihedral_angle_d13.866751
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9009-1.93370.22791550.164212821437
1.9337-1.96880.21731300.15512691399
1.9688-2.00670.1921330.153412691402
2.0067-2.04760.19051330.146712881421
2.0476-2.09220.20281300.13812731403
2.0922-2.14080.17681280.142112991427
2.1408-2.19440.15871290.132512571386
2.1944-2.25370.17451500.138712691419
2.2537-2.320.19011570.142912571414
2.32-2.39490.19791340.146712911425
2.3949-2.48040.19391470.136812521399
2.4804-2.57970.17481360.146913031439
2.5797-2.69710.17211590.146812631422
2.6971-2.83930.17251640.152612631427
2.8393-3.01710.19331540.150812821436
3.0171-3.250.17191390.154412881427
3.25-3.57680.17471370.143813131450
3.5768-4.09390.16911210.132613171438
4.0939-5.15610.15561370.13113381475
5.1561-39.3030.18261590.173413721531
Refinement TLS params.Method: refined / Origin x: 10.474 Å / Origin y: 39.9509 Å / Origin z: 27.5964 Å
111213212223313233
T0.1095 Å20.0004 Å2-0.024 Å2-0.1557 Å20.0064 Å2--0.1016 Å2
L1.3151 °2-0.6558 °2-0.3685 °2-1.658 °20.0822 °2--0.7318 °2
S0.0743 Å °0.2606 Å °-0.0522 Å °-0.2046 Å °-0.0643 Å °0.1116 Å °-0.0012 Å °-0.0962 Å °-0.0237 Å °
Refinement TLS groupSelection details: ALL

+
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