[English] 日本語
Yorodumi
- PDB-2j0r: Structure of the haem-chaperone Proteobacteria-protein HemS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j0r
TitleStructure of the haem-chaperone Proteobacteria-protein HemS
ComponentsHEMIN TRANSPORT PROTEIN HEMS
KeywordsTRANSPORT PROTEIN / PROTEOBACTERIA / IRON TRANSPORT
Function / homology
Function and homology information


Haemin-degrading HemS/ChuX domain / Haemin-degrading HemS.ChuX domain / HemS/ChuS/ChuX like domains / Heme iron utilization protein-like fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Hemin transport protein HemS
Similarity search - Component
Biological speciesYERSINIA ENTEROCOLITICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchneider, S. / Sharp, K.H. / Barker, P.D. / Paoli, M.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: An Induced Fit Conformational Change Underlies the Binding Mechanism of the Heme Transport Proteobacteria-Protein Hems.
Authors: Schneider, S. / Sharp, K.H. / Barker, P.D. / Paoli, M.
#1: Journal: Acta Crystallogr., Sect.F / Year: 2005
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of the Haem-Binding Protein Hems from Yersinia Enterocolitica.
Authors: Schneider, S. / Paoli, M.
History
DepositionAug 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEMIN TRANSPORT PROTEIN HEMS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,80912
Polymers39,2451
Non-polymers1,56411
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.022, 68.269, 73.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein HEMIN TRANSPORT PROTEIN HEMS / HEMS


Mass: 39244.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: WA-C / Plasmid: PGAT2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31517

-
Non-polymers , 6 types, 145 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsASN 162 IS ILE IN THE SEQUENCE FILE P31517. COMPARISON OF MULTIPLE SEQUENCE ALIGNMENTS OF HEMS ...ASN 162 IS ILE IN THE SEQUENCE FILE P31517. COMPARISON OF MULTIPLE SEQUENCE ALIGNMENTS OF HEMS HOMOLOGUES AND HEMS FROM Y.ENTEROCOLITICA STRAIN 8081 SEQUENCED AT THE SANGER INSTITUTE, SHOW ASN AT THIS POSITION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.55 %
Crystal growDetails: 100MM BICINE PH 9, 2.45M AMMONIUM SULPHATE, 5% PEG 400

-
Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 13, 2006 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 25260 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J0P

2j0p


Resolution: 1.9→50.06 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.491 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1289 5.1 %RANDOM
Rwork0.189 ---
obs0.191 23971 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--1.78 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 86 134 2886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212793
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9463753
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9315335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27524.626147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63715465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0761520
X-RAY DIFFRACTIONr_chiral_restr0.1830.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022100
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21227
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21841
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8641.51697
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07322653
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.80931223
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8364.51097
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 90 -
Rwork0.204 1747 -
obs--100 %
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)
12.5368-0.0106-0.36971.7966-0.84853.4119-0.0552-0.1534-0.20790.024-0.0325-0.13860.31520.40110.08770.05730.0214-0.00720.08530.00280.03252.5583-28.862116.5631
20.57120.5137-0.27461.182-0.58161.6713-0.0170.02260.0854-0.00560.03260.0637-0.0653-0.0421-0.01560.04690.0003-0.01210.08770.00920.0632-11.1781-26.51692.5118
34.445-2.7263-0.21487.82140.41230.9703-0.03550.09470.2265-0.0873-0.0141-0.0017-0.0712-0.07720.04950.0843-0.0036-0.02020.06980.01380.0367-15.9988-21.5119-4.5349
41.79890.62880.6960.56060.13131.99760.01490.012-0.108-0.02080.0004-0.01620.0152-0.0367-0.01530.1027-0.003-0.0010.05380.0140.0894-12.7494-24.35043.5797
51.03050.0289-0.21640.59320.1951.3926-0.05210.09940.0741-0.07180.0454-0.04540.01350.08640.00670.0484-0.0118-0.00150.06430.01340.0509-3.8593-22.90832.2588
616.98965.9858-13.19313.6643-5.160112.28330.23560.19670.76450.10270.21590.4066-0.401-0.1587-0.45150.1055-0.027-0.00880.0525-0.00750.0576-5.9146-16.295919.5107
76.4795-0.65162.46262.3513-0.8314.32460.0002-0.33920.69880.05810.31080.0499-0.3111-0.2396-0.311-0.1238-0.00580.13670.1876-0.18890.0888-38.9598-31.179114.7797
80.70280.0927-0.05190.66120.47361.7410.0098-0.0385-0.11620.0832-0.03730.04220.2926-0.08810.02750.0772-0.0174-0.00340.0436-0.00440.0376-21.565-43.49593.7036
91.29370.25010.12950.8054-0.28372.1280.0318-0.0956-0.01770.08-0.05210.09740.1351-0.18380.02030.1217-0.0310.01830.0583-0.02920.0726-23.8975-40.87857.0837
100.94440.2730.64650.36050.07393.195-0.0712-0.03010.0856-0.0065-0.06640.19160.0006-0.38090.13750.0454-0.03450.00940.1029-0.02650.0499-28.7011-37.61267.1901
114.9879-1.89040.35137.7859-4.23645.91440.10170.0681-0.1531-0.1135-0.22210.14370.281-0.32340.12040.0223-0.090.00570.1145-0.10.0308-33.6264-44.3063-1.2534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 48
2X-RAY DIFFRACTION2A49 - 77
3X-RAY DIFFRACTION3A78 - 87
4X-RAY DIFFRACTION4A88 - 123
5X-RAY DIFFRACTION5A124 - 159
6X-RAY DIFFRACTION6A160 - 171
7X-RAY DIFFRACTION7A180 - 216
8X-RAY DIFFRACTION8A217 - 274
9X-RAY DIFFRACTION9A275 - 297
10X-RAY DIFFRACTION10A298 - 321
11X-RAY DIFFRACTION11A322 - 341

+
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://pdbjlvh1.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