[English] 日本語
Yorodumi
- PDB-2xuv: The structure of HdeB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xuv
TitleThe structure of HdeB
ComponentsHDEB
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


cellular stress response to acidic pH / response to acidic pH / unfolded protein binding / outer membrane-bounded periplasmic space
Similarity search - Function
HNS-dependent expression B / HNS-dependent expression A / HNS-dependent expression A/B / HNS-dependent expression A/B superfamily / HdeA/HdeB family / 10k-s Protein, Hypothetical Protein A; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Acid stress chaperone HdeB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsNaismith, J.H. / Wang, W.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Salt Bridges Regulate Both Dimer Formation and Monomeric Flexibility in Hdeb and May Have a Role in Periplasmic Chaperone Function.
Authors: Wang, W. / Rasmussen, T. / Harding, A.J. / Booth, N.A. / Booth, I.R. / Naismith, J.H.
History
DepositionOct 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Dec 21, 2011Group: Database references
Revision 1.4Jan 25, 2012Group: Other
Revision 1.5Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: HDEB
B: HDEB
C: HDEB
D: HDEB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3546
Polymers37,1624
Non-polymers1922
Water4,828268
1
A: HDEB
B: HDEB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6773
Polymers18,5812
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-42.9 kcal/mol
Surface area8090 Å2
MethodPISA
2
C: HDEB
D: HDEB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6773
Polymers18,5812
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-20.9 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.920, 86.500, 48.500
Angle α, β, γ (deg.)90.00, 112.54, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
HDEB / 10K-L PROTEIN


Mass: 9290.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0AET2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PERIPLASMIC LEADER SEQUENCE IS CLEAVED OFF DURING SYNTHESIS. HDEB IS FOUND IN THE PERIPLASM. ...THE PERIPLASMIC LEADER SEQUENCE IS CLEAVED OFF DURING SYNTHESIS. HDEB IS FOUND IN THE PERIPLASM. MNISSLRKAFIFMGAVAALSLVNAQSALA

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.24 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.5→33 Å / Num. obs: 58562 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 2.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.7 / % possible all: 94.5

-
Processing

Software
NameVersionClassification
REFMAC5.6.0086refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→32.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.03 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TYR 64 IN THE A SUBUNIT AND TO SOME EXTENT IN THE B SUBUNIT SHOWS EVIDENCE OF METHYLATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.19544 2943 5 %RANDOM
Rwork0.18149 ---
obs0.18218 55610 95.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.701 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.04 Å2
2---0.06 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 10 268 2583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222516
X-RAY DIFFRACTIONr_bond_other_d0.0010.021641
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9883457
X-RAY DIFFRACTIONr_angle_other_deg0.90234106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10927.094117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4915415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 205 -
Rwork0.193 4060 -
obs--94.53 %
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)
13.28590.2945-2.11024.04871.98955.9203-0.0321-0.12220.06650.2639-0.0025-0.08380.26470.08330.03460.042-0.0043-0.01330.0139-0.00490.0193-30.028-5.095-8.618
28.58832.7778-2.5254.3926-0.0362.925-0.01350.0078-0.16850.03470.00990.15540.0772-0.24540.00360.0175-0.0052-0.00750.03860.00890.0239-39.855-15.074-10.549
33.4694-2.42621.54034.6372-2.34422.18360.13040.0593-0.156-0.1254-0.06790.31930.1333-0.1438-0.06250.0773-0.0209-0.02650.09340.0010.0478-43.471-17.863-19.138
43.74922.57821.48575.2711.50093.4871-0.0287-0.10060.32960.0317-0.06670.5228-0.0976-0.1390.09530.01870.02190.00740.0469-0.03010.1178-40.38-1.251-9.954
52.17930.2062-0.75992.79520.13312.18130.04990.02950.0542-0.1202-0.0209-0.2175-0.04140.0495-0.0290.02640.00890.01010.01990.00120.0195-25.624-13.81-14.234
67.0148-0.8298-2.54393.45792.32954.4854-0.18410.1613-0.5186-0.09420.02970.22510.4909-0.42770.15440.1605-0.0412-0.02810.12680.02110.1219-38.58-25.591-11.564
77.38963.4192-5.39152.5658-2.81495.8118-0.0247-0.4012-0.3133-0.0859-0.1733-0.3390.17250.49940.19790.0630.03320.01220.09530.01740.0689-22.079-23.503-7.585
88.5583-3.0936-0.5026.5388-0.85387.56170.01460.3022-0.3233-0.5289-0.0112-0.20320.49360.3031-0.00340.15240.03890.05640.0875-0.02410.0706-21.104-22.576-18.526
93.45862.13360.36934.56060.14671.5347-0.02770.22340.0797-0.27980.01270.2585-0.0222-0.01140.01490.0679-0.0123-0.02130.0498-0.00620.0168-23.96512.833-12.783
109.118-0.45678.545220.3249-14.235517.4088-1.52580.21150.90851.115-0.0663-1.1406-2.2290.26111.59220.8112-0.19350.00760.35490.02740.2625-10.8424.748-10.205
113.6691.9952.48832.8981.81244.1331-0.1051-0.14250.3433-0.2454-0.12520.6019-0.193-0.340.23030.09110.0204-0.05190.08470.00290.1507-28.5320.396-9.14
1216.13261.442716.634910.5704-1.728646.2839-0.67550.58861.9443-0.74060.28170.3956-2.87110.11220.39370.4137-0.0065-0.11890.12050.10530.4935-27.91925.365-15.81
131.92421.80960.13964.5566-0.16721.01950.01680.0254-0.11910.01950.0009-0.0887-0.02150.0468-0.01770.0339-0.0137-0.00020.0502-0.01680.0275-17.3696.221-9.549
142.0051-0.58383.23259.40790.02215.31710.08940.37080.1218-0.6228-0.2097-0.84840.06210.61930.12030.0932-0.04730.08230.28320.02530.1671-6.09916.851-13.273
158.03852.184-3.78637.7806-0.42297.5610.1710.4978-0.3398-0.30630.0013-0.8142-0.09930.1037-0.17230.03490.01190.02780.1419-0.02060.2003-10.342-2.411-12.107
165.39770.8889-1.566211.5618-0.19678.60490.2287-0.234-0.11040.4459-0.1052-1.31210.04670.6201-0.12350.0428-0.0182-0.07420.14420.0120.256-7.8262.726-5.121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 48
2X-RAY DIFFRACTION2A49 - 66
3X-RAY DIFFRACTION3A67 - 77
4X-RAY DIFFRACTION4A78 - 100
5X-RAY DIFFRACTION5B30 - 57
6X-RAY DIFFRACTION6B58 - 71
7X-RAY DIFFRACTION7B72 - 91
8X-RAY DIFFRACTION8B92 - 100
9X-RAY DIFFRACTION9C32 - 59
10X-RAY DIFFRACTION10C60 - 70
11X-RAY DIFFRACTION11C71 - 96
12X-RAY DIFFRACTION12C97 - 101
13X-RAY DIFFRACTION13D32 - 59
14X-RAY DIFFRACTION14D60 - 78
15X-RAY DIFFRACTION15D79 - 93
16X-RAY DIFFRACTION16D94 - 101

+
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