[English] 日本語
Yorodumi
- PDB-4nav: Crystal structure of hypothetical protein XCC2798 from Xanthomona... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nav
TitleCrystal structure of hypothetical protein XCC2798 from Xanthomonas campestris, Target EFI-508608
ComponentsHYPOTHETICAL PROTEIN XCC279Hypothesis
KeywordsHYDROLASE / Structural Genomics / Enzyme Function Initiative
Function / homology
Function and homology information


3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / lipopolysaccharide biosynthetic process / metal ion binding
Similarity search - Function
KdsC family / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Glenn, A.S. / Chowdhury, S. ...Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Glenn, A.S. / Chowdhury, S. / Evans, B. / Zhao, S.C. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Stead, M. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of hypothetical protein XCC2798 from Xanthomonas campestris, Target EFI-508608
Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Zhao, S. / Hillerich, B. / ...Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Zhao, S. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Stead, M. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: HYPOTHETICAL PROTEIN XCC279
A: HYPOTHETICAL PROTEIN XCC279
B: HYPOTHETICAL PROTEIN XCC279
C: HYPOTHETICAL PROTEIN XCC279


Theoretical massNumber of molelcules
Total (without water)78,2694
Polymers78,2694
Non-polymers00
Water66737
1
D: HYPOTHETICAL PROTEIN XCC279
C: HYPOTHETICAL PROTEIN XCC279

D: HYPOTHETICAL PROTEIN XCC279
C: HYPOTHETICAL PROTEIN XCC279


Theoretical massNumber of molelcules
Total (without water)78,2694
Polymers78,2694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9880 Å2
ΔGint-43 kcal/mol
Surface area26400 Å2
MethodPISA
2
A: HYPOTHETICAL PROTEIN XCC279
B: HYPOTHETICAL PROTEIN XCC279

A: HYPOTHETICAL PROTEIN XCC279
B: HYPOTHETICAL PROTEIN XCC279


Theoretical massNumber of molelcules
Total (without water)78,2694
Polymers78,2694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9580 Å2
ΔGint-45 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.903, 156.017, 111.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22B
13D
23C
14A
24B
15A
25C
16B
26C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSERDA2 - 1812 - 181
21PROPROSERSERAB2 - 1812 - 181
12METMETPHEPHEDA1 - 1801 - 180
22METMETPHEPHEBC1 - 1801 - 180
13METMETALAALADA1 - 1821 - 182
23METMETALAALACD1 - 1821 - 182
14PROPROPHEPHEAB2 - 1802 - 180
24PROPROPHEPHEBC2 - 1802 - 180
15PROPROSERSERAB2 - 1812 - 181
25PROPROSERSERCD2 - 1812 - 181
16METMETPHEPHEBC1 - 1801 - 180
26METMETPHEPHECD1 - 1801 - 180

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
HYPOTHETICAL PROTEIN XCC279 / Hypothesis


Mass: 19567.291 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: ATCC 33913 / Gene: XCC2798 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P716
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 85mM Tris-HCl, pH 8.5 0.17M sodium acetate 25.5% PEG4000,15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Oct 12, 2013
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.69→111.51 Å / Num. all: 21987 / Num. obs: 21866 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.2
Reflection shellResolution: 2.69→2.83 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3145 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3N1U

3n1u


Resolution: 2.69→78.01 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.852 / SU B: 32.272 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1095 5.2 %RANDOM
Rwork0.24358 ---
obs0.24516 20128 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2--1.68 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.69→78.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5331 0 0 37 5368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195427
X-RAY DIFFRACTIONr_bond_other_d0.0060.025188
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9627396
X-RAY DIFFRACTIONr_angle_other_deg1.196311827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20123.932234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60915804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1131541
X-RAY DIFFRACTIONr_chiral_restr0.080.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216354
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021227
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_it1.4892.5012900
X-RAY DIFFRACTIONr_mcbond_other1.4892.5012899
X-RAY DIFFRACTIONr_mcangle_it2.4473.7483618
X-RAY DIFFRACTIONr_mcangle_other2.4473.7483619
X-RAY DIFFRACTIONr_scbond_it1.8622.6362527
X-RAY DIFFRACTIONr_scbond_other1.8612.6362528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0393.883779
X-RAY DIFFRACTIONr_long_range_B_refined4.51519.3915798
X-RAY DIFFRACTIONr_long_range_B_other4.51519.3925799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D100280.08
12A100280.08
21D97920.09
22B97920.09
31D96940.1
32C96940.1
41A98930.08
42B98930.08
51A97700.11
52C97700.11
61B98220.09
62C98220.09
LS refinement shellResolution: 2.688→2.758 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 90 -
Rwork0.316 1490 -
obs--99.5 %
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)
11.03-0.36411.30190.8449-0.34162.34940.24190.0589-0.0791-0.03710.04980.08510.37040.1643-0.29180.16420.0322-0.15410.07240.01190.2567-6.337321.87547.4112
22.3568-0.3186-0.45230.41410.13051.18110.26890.24210.63280.023-0.0588-0.0118-0.19380.021-0.21010.230.04260.29980.04860.12160.526810.658264.36659.0753
31.74820.04661.19651.23890.82772.61210.12030.07160.5933-0.0188-0.1190.1005-0.2059-0.1871-0.00130.18520.06610.24260.03950.09530.4646-18.893764.209816.959
42.3466-0.90490.09690.7306-0.05472.88480.1594-0.3127-0.2764-0.11940.03720.11860.2903-0.6983-0.19660.1516-0.1001-0.16560.23720.0880.2376-20.832621.420834.3147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 182
2X-RAY DIFFRACTION2A2 - 182
3X-RAY DIFFRACTION3B1 - 181
4X-RAY DIFFRACTION4C1 - 182

+
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