[English] 日本語
Yorodumi
- PDB-3hpe: Crystal structure of yceI (HP1286) from Helicobacter pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hpe
TitleCrystal structure of yceI (HP1286) from Helicobacter pylori
ComponentsConserved hypothetical secreted protein
KeywordsTRANSPORT PROTEIN / HP1286 / HELICOBACTER PYLORI / ERUCAMIDE / fatty-acid binding
Function / homology
Function and homology information


Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like / Lipid/polyisoprenoid-binding, YceI-like superfamily / YceI-like domain / YceI-like domain / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(13Z)-docos-13-enamide / Conserved hypothetical secreted protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSisinni, L. / Cendron, L. / Zanotti, G.
Citation
Journal: Febs J. / Year: 2010
Title: Helicobacter pylori acidic stress response factor HP1286 is a YceI homolog with new binding specificity.
Authors: Sisinni, L. / Cendron, L. / Favaro, G. / Zanotti, G.
#1: Journal: Protein Sci. / Year: 2005
Title: Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8.
Authors: Handa, N. / Terada, T. / Doi-Katayama, Y. / Hirota, H. / Tame, J.R. / Park, S.Y. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
#2: Journal: Biochemistry / Year: 2005
Title: Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II.
Authors: Toms, A.V. / Haas, A.L. / Park, J.H. / Begley, T.P. / Ealick, S.E.
History
DepositionJun 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Conserved hypothetical secreted protein
B: Conserved hypothetical secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0004
Polymers37,3252
Non-polymers6752
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-2.6 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.936, 61.312, 88.316
Angle α, β, γ (deg.)90.00, 92.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

-
Components

#1: Protein Conserved hypothetical secreted protein


Mass: 18662.395 Da / Num. of mol.: 2 / Fragment: UNP residues 18-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: CCUG17874 / Gene: HP1286 / Plasmid: pET151-HP1286 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1CRX8
#2: Chemical ChemComp-ERU / (13Z)-docos-13-enamide / Erucamide / erucylamide


Mass: 337.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H43NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris-HCl, 2M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→50.3 Å / Num. all: 19367 / Num. obs: 19367 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 10.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 4.9 / Num. unique all: 2823 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WUB

1wub


Resolution: 2.1→50.3 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.711 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.293 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27425 1519 7.8 %RANDOM
Rwork0.21242 ---
all0.21708 19367 --
obs0.21708 19367 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.54 Å2
Baniso -1Baniso -2Baniso -3
1-3.35 Å20 Å22.06 Å2
2---1.27 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2632 0 48 79 2759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9693650
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.69625.323124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49115518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.502158
X-RAY DIFFRACTIONr_chiral_restr0.1290.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212012
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_it0.6651.51630
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21722636
X-RAY DIFFRACTIONr_scbond_it2.36831102
X-RAY DIFFRACTIONr_scangle_it3.8014.51014
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
656medium positional0.160.5
660loose positional0.285
656medium thermal2.592
660loose thermal2.9710
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 103 -
Rwork0.23 1284 -
obs-2258 99.78 %
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)
10.7872-1.875-0.80226.24951.11953.20390.1097-0.07330.0562-0.3180.07630.0675-0.24120.2372-0.1860.065-0.03570.0170.242-0.00730.22777.3473-4.573928.0847
22.91812.0026-0.7578.71411.72082.8706-0.2187-0.061-0.1921-0.06190.22770.0110.32810.1863-0.0090.0510.01990.01990.19610.01350.17355.4396-14.362931.2895
36.13152.78670.38343.36170.19766.09880.0391-0.41960.17260.34330.0982-0.3795-0.61440.6867-0.13730.118-0.0157-0.04880.2432-0.09570.141513.07590.898740.0973
43.83532.46692.40135.19594.92977.8158-0.1908-0.1910.1679-0.1314-0.07540.46390.075-0.50790.26610.03820.00990.00250.25890.04790.2486-3.9134-10.988837.7639
55.6033-0.663-5.1725.17463.026113.0122-0.27940.2997-0.267-0.9425-0.06470.01590.25180.14210.34410.32910.0168-0.09170.04730.00540.17426.683-21.441418.2083
68.297-14.7991-13.73627.342125.552227.26870.18390.1533-0.224-0.3376-0.37870.5959-0.3982-0.50670.19480.0405-0.0534-0.02640.20890.020.27621.2782-9.907127.3825
73.0311-2.2524-4.4148.79642.05426.64450.24720.11580.1850.07250.12460.1517-0.4773-0.2082-0.37170.11660.01420.08760.0735-0.01240.12211.43827.607339.7471
87.9532-13.3115-6.133625.577611.75467.42460.13550.09880.0014-0.3256-0.07360.0856-0.08980.1846-0.06190.0494-0.0489-0.05570.22450.01370.22186.4126-12.399125.9728
90.8665-0.5671-0.66599.96722.49443.34540.3457-0.14930.22640.3518-0.2052-0.3134-0.48470.0385-0.14050.2493-0.11010.12290.1403-0.07350.173413.045412.950320.1489
103.68034.74530.50311.12311.07331.52560.1522-0.3070.140.1952-0.18240.31150.180.06650.03020.102-0.0640.03180.2156-0.01330.156611.9975-5.444917.0399
114.3971-3.78360.39999.8088-2.3153.48820.25580.00220.6497-0.29480.0899-0.4642-0.87730.0785-0.34560.4961-0.15940.19340.1025-0.0560.18413.398316.765913.3727
125.8014-0.70470.8037.7452-3.28813.58890.1455-0.27060.0622-0.3347-0.1301-0.44940.08390.7299-0.01540.0406-0.05830.00560.3169-0.0360.234224.2809-5.453314.0769
134.4574-4.6024-1.39048.0462-1.37412.93980.47110.28650.0636-0.5554-0.19880.0999-0.2855-0.1462-0.27230.4309-0.14610.1070.1684-0.00770.188112.579210.76964.4305
141.49530.4436-0.99525.39587.991413.7070.23050.02820.19430.131-0.01760.0083-0.057-0.0571-0.2130.4293-0.04830.09020.083-0.00240.23635.11318.854922.0811
154.2539-4.7544-2.547215.6665.16323.05590.15880.07930.0346-0.4545-0.1289-0.1617-0.03680.0358-0.02990.1117-0.0332-0.02290.1382-0.01270.094213.7139-4.47285.3557
160.9278-1.4034-0.320527.786610.82884.67970.1346-0.04670.1241-0.0821-0.36220.3226-0.2072-0.17880.22760.1457-0.01890.00220.10610.01490.092210.02254.41215.4775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 39
2X-RAY DIFFRACTION2A40 - 69
3X-RAY DIFFRACTION3A70 - 101
4X-RAY DIFFRACTION4A102 - 125
5X-RAY DIFFRACTION5A126 - 141
6X-RAY DIFFRACTION6A142 - 152
7X-RAY DIFFRACTION7A153 - 171
8X-RAY DIFFRACTION8A172 - 181
9X-RAY DIFFRACTION9B18 - 32
10X-RAY DIFFRACTION10B33 - 48
11X-RAY DIFFRACTION11B49 - 73
12X-RAY DIFFRACTION12B74 - 95
13X-RAY DIFFRACTION13B96 - 122
14X-RAY DIFFRACTION14B123 - 146
15X-RAY DIFFRACTION15B147 - 164
16X-RAY DIFFRACTION16B165 - 181

+
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