[English] 日本語
Yorodumi
- PDB-3ihs: Crystal Structure of a Phosphocarrier Protein HPr from Bacillus a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ihs
TitleCrystal Structure of a Phosphocarrier Protein HPr from Bacillus anthracis str. Ames
ComponentsPhosphocarrier protein HPr
KeywordsTRANSPORT PROTEIN / phosphocarrier protein HPr / dimerization domain swap beta strand / IDP01131 / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID
Function / homology
Function and homology information


Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / PTS HPR domain serine phosphorylation site signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr / Phosphocarrier protein HPr
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å
AuthorsBrunzelle, J.S. / Anderson, S.M. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of a Phosphocarrier Protein HPr from Bacillus anthracis str. Ames
Authors: Brunzelle, J.S. / Anderson, S.M. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphocarrier protein HPr
B: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)23,5672
Polymers23,5672
Non-polymers00
Water3,351186
1
A: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)11,7841
Polymers11,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)11,7841
Polymers11,7841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.840, 40.840, 139.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A-2 - 82
2116B-2 - 82

-
Components

#1: Protein Phosphocarrier protein HPr


Mass: 11783.522 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS5001, BA_5381, GBAA5381, GBAA_5381, ptsH-2, ptsH2 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81X62, UniProt: A0A6L7HPZ9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350 20%, K dihydrogen Phosphate 0.2M, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.97857
SYNCHROTRONAPS 21-ID-D21.09721
Detector
TypeIDDetectorDateDetails
RAYONIX MX-3001CCDMar 14, 2009Be Lens
RAYONIX MX-3002CCDMar 21, 2009Mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond 111SINGLE WAVELENGTHMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.978571
21.097211
ReflectionResolution: 1.15→23.2 Å / Num. all: 204840 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 17.12
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.28 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.62 / Num. unique all: 2297 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIXmodel building
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.15→23.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.087 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18499 2354 5 %RANDOM
Rwork0.15574 ---
obs0.15716 45191 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.017 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.15→23.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 0 199 1562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221375
X-RAY DIFFRACTIONr_bond_other_d0.0070.02933
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9711866
X-RAY DIFFRACTIONr_angle_other_deg0.93532320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3785195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05425.55654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.86515277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.301157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
X-RAY DIFFRACTIONr_nbd_refined0.2680.2301
X-RAY DIFFRACTIONr_nbd_other0.2130.2952
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2718
X-RAY DIFFRACTIONr_nbtor_other0.0910.2733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4882.51070
X-RAY DIFFRACTIONr_mcbond_other0.7422.5364
X-RAY DIFFRACTIONr_mcangle_it2.97331431
X-RAY DIFFRACTIONr_scbond_it3.8194531
X-RAY DIFFRACTIONr_scangle_it4.8815424
X-RAY DIFFRACTIONr_rigid_bond_restr1.72142623
X-RAY DIFFRACTIONr_sphericity_free16.84210200
X-RAY DIFFRACTIONr_sphericity_bonded7.084102284
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 960 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.385
loose thermal1.8110
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 173 -
Rwork0.206 3193 -
obs--94.18 %

+
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