[English] 日本語
Yorodumi
- PDB-3civ: Crystal structure of the endo-beta-1,4-mannanase from Alicyclobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3civ
TitleCrystal structure of the endo-beta-1,4-mannanase from Alicyclobacillus acidocaldarius
ComponentsEndo-beta-1,4-mannanase
KeywordsHYDROLASE / TIM BARREL
Function / homology: / Glycoside Hydrolase Family 113 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Endo-beta-1,4-mannanase
Function and homology information
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsMa, Y. / Zhang, Y. / Xue, Y.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Biochemical and Structural Characterization of the Intracellular Mannanase AaManA of Alicyclobacillus acidocaldarius Reveals a Novel Glycoside Hydrolase Family Belonging to Clan GH-A
Authors: Zhang, Y. / Ju, J. / Peng, H. / Gao, F. / Zhou, C. / Zeng, Y. / Xue, Y. / Li, Y. / Henrissat, B. / Gao, G.F. / Ma, Y.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary X-ray study of native and selenomethionyl beta-1,4-mannanase AaManA from Alicyclobacillus acidocaldarius Tc-12-31
Authors: Zhang, Y. / Gao, F. / Xue, Y. / Zeng, Y. / Peng, H. / Qi, J. / Ma, Y.
History
DepositionMar 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endo-beta-1,4-mannanase


Theoretical massNumber of molelcules
Total (without water)38,8041
Polymers38,8041
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.338, 75.554, 88.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Endo-beta-1,4-mannanase


Mass: 38803.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Strain: Tc-12-31 / Gene: AamanA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5H1I6, mannan endo-1,4-beta-mannosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 1.9 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium dihydrogen phosphate, 0.1M sodium citrate (pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→35.07 Å / Num. obs: 23386 / % possible obs: 97.3 % / Redundancy: 6.92 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 10.2 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→35.07 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.86 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21208 1206 5.2 %RANDOM
Rwork0.1737 ---
obs0.17571 22180 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.037 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---0.63 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 0 221 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212605
X-RAY DIFFRACTIONr_angle_refined_deg1.0861.9213541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57522.595131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80915387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.611522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022082
X-RAY DIFFRACTIONr_nbd_refined0.1820.21314
X-RAY DIFFRACTIONr_nbtor_refined0.30.21770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.220
X-RAY DIFFRACTIONr_mcbond_it0.5771.51623
X-RAY DIFFRACTIONr_mcangle_it0.92122511
X-RAY DIFFRACTIONr_scbond_it1.41831181
X-RAY DIFFRACTIONr_scangle_it2.2824.51030
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 84 -
Rwork0.205 1435 -
obs--86.75 %

+
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