[English] 日本語
Yorodumi
- PDB-4fcu: 1.9 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cyti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fcu
Title1.9 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cytidylyltransferase (kdsB) from Acinetobacter baumannii without His-Tag Bound to the Active Site
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / lipopolysaccharide biosynthetic process / 3-deoxy-manno-octulosonate cytidylyltransferase activity
Function / homology
Function and homology information


3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate cytidylyltransferase activity / CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / lipopolysaccharide biosynthetic process / cytoplasm
Similarity search - Function
3-deoxy-D-manno-octulosonate cytidylyltransferase / Acylneuraminate cytidylyltransferase / Cytidylyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.9 Angstrom Crystal Structure of 3-deoxy-manno-octulosonate Cytidylyltransferase (kdsB) from Acinetobacter baumannii without His-Tag Bound to the Active Site.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)28,4261
Polymers28,4261
Non-polymers00
Water2,990166
1
A: 3-deoxy-manno-octulosonate cytidylyltransferase

A: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)56,8532
Polymers56,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3030 Å2
ΔGint-11 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.542, 40.155, 54.710
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number5
Space group name H-MC121
DetailsChains A and symmetry related -X, Y, -Z one form a dimer.

-
Components

#1: Protein 3-deoxy-manno-octulosonate cytidylyltransferase / CMP-2-keto-3-deoxyoctulosonic acid synthase / CKS / CMP-KDO synthase


Mass: 28426.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 17978 / Gene: A1S_1557, kdsB / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: A3M4Z0, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 7.4mG/mL, 0.25M Sodium cloride, Tris-HCl (pH 8.3), Screen: JCSG+ (H8), 0.2M Sodium chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 20, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 18315 / Num. obs: 18315 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / Num. unique all: 909 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3POL

3pol


Resolution: 1.9→29.52 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.736 / SU ML: 0.117
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24233 940 5.1 %RANDOM
Rwork0.18719 ---
all0.18999 17342 --
obs0.18999 17342 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.357 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å21.17 Å2
2---1.56 Å20 Å2
3---2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 0 166 2159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222118
X-RAY DIFFRACTIONr_bond_other_d0.0010.021450
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.9782886
X-RAY DIFFRACTIONr_angle_other_deg0.85133546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9455269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67224.272103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06415380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.671519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02405
X-RAY DIFFRACTIONr_mcbond_it1.1291.51321
X-RAY DIFFRACTIONr_mcbond_other0.3451.5520
X-RAY DIFFRACTIONr_mcangle_it1.91722154
X-RAY DIFFRACTIONr_scbond_it3.0763797
X-RAY DIFFRACTIONr_scangle_it5.0344.5732
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 71 -
Rwork0.222 1254 -
obs-1254 99.25 %
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)
13.62483.0292-0.58315.73450.17921.1542-0.1230.2290.1744-0.33010.16090.3042-0.229-0.0187-0.03790.13020.0291-0.00610.07190.0010.020527.297814.9599-18.8649
21.38120.137-0.1440.67620.19081.03230.00140.0892-0.1234-0.0823-0.03250.0146-0.0682-0.00810.03110.04370.0108-0.00450.0278-0.00520.013320.41536.195-14.1968
33.8184-0.65040.03433.0076-0.53291.2478-0.0909-0.20740.36050.18820.04530.0504-0.2542-0.00130.04560.0628-0.0037-0.00750.0561-0.03180.04815.294819.37233.0053
41.3228-0.396-0.22460.99310.11380.530.05740.1541-0.0215-0.0476-0.05110.0666-0.0524-0.0408-0.00630.046-0.00250.00690.03850.00670.01466.169510.5902-7.1041
52.59061.58840.29491.02360.19930.04540.1025-0.09140.08510.005-0.0910.02230.0129-0.0195-0.01160.1870.0230.00570.1237-0.02260.055431.374820.5235-8.6358
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 33
2X-RAY DIFFRACTION2A34 - 135
3X-RAY DIFFRACTION3A136 - 170
4X-RAY DIFFRACTION4A171 - 227
5X-RAY DIFFRACTION5A228 - 253

+
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