[English] 日本語
Yorodumi
- PDB-5cr9: Crystal structure of ABC-type Fe3+-hydroxamate transport system f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cr9
TitleCrystal structure of ABC-type Fe3+-hydroxamate transport system from Saccharomonospora viridis DSM 43017
ComponentsABC-type Fe3+-hydroxamate transport system, periplasmic component
KeywordsTRANSPORT PROTEIN / Inorganic ion transport / TroA-like / ABC transport of ferric siderophores and metal ions such as Mn2+ / Fe3+ / Cu2+ and/or Zn2+ / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / : / ABC-type Fe3+-hydroxamate transport system, periplasmic component
Similarity search - Component
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsNocek, B. / Cuff, M. / Mack, J. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: Crystal structure of ABC-type Fe3+-hydroxamate transport system from Saccharomonospora viridis DSM 43017
Authors: Nocek, B. / Cuff, M. / Mack, J. / Endres, M. / Joachimiak, A.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 23, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC-type Fe3+-hydroxamate transport system, periplasmic component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5955
Polymers33,2091
Non-polymers3864
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.690, 56.855, 62.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein ABC-type Fe3+-hydroxamate transport system, periplasmic component


Mass: 33208.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (strain ATCC 15386 / DSM 43017 / JCM 3036 / NBRC 12207 / P101) (bacteria)
Strain: ATCC 15386 / DSM 43017 / JCM 3036 / NBRC 12207 / P101
Gene: Svir_21280 / Production host: Escherichia coli (E. coli) / References: UniProt: C7MWN7
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 40 % MPD, 0.1 M Tris pH 8.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2012
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→37.57 Å / Num. obs: 33513 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 29.76
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.669 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→37.569 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.09 / Phase error: 14.91 / Stereochemistry target values: ML
Details: The identity of metal atom (Mn 2+) was determined based on the distances to donor atoms, coordination number. The ligand identity was guessed based on the shape of the density
RfactorNum. reflection% reflectionSelection details
Rfree0.1722 3203 5.06 %Random Selection
Rwork0.1458 ---
obs0.1471 31765 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→37.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 23 278 2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092294
X-RAY DIFFRACTIONf_angle_d1.2683147
X-RAY DIFFRACTIONf_dihedral_angle_d13.222849
X-RAY DIFFRACTIONf_chiral_restr0.051372
X-RAY DIFFRACTIONf_plane_restr0.007425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6979-1.72330.25681430.2212472X-RAY DIFFRACTION93
1.7233-1.75020.23611380.20722614X-RAY DIFFRACTION100
1.7502-1.77890.23561350.18832634X-RAY DIFFRACTION100
1.7789-1.80960.23071450.17622587X-RAY DIFFRACTION100
1.8096-1.84250.18791460.16282631X-RAY DIFFRACTION100
1.8425-1.87790.17211540.1562604X-RAY DIFFRACTION100
1.8779-1.91620.17631280.15342642X-RAY DIFFRACTION100
1.9162-1.95790.16551230.14062661X-RAY DIFFRACTION100
1.9579-2.00340.18971660.13452577X-RAY DIFFRACTION100
2.0034-2.05350.15721310.13092634X-RAY DIFFRACTION100
2.0535-2.1090.1281370.12942650X-RAY DIFFRACTION100
2.109-2.17110.14141500.12872601X-RAY DIFFRACTION100
2.1711-2.24120.17911300.12792641X-RAY DIFFRACTION100
2.2412-2.32130.17521500.12872596X-RAY DIFFRACTION100
2.3213-2.41420.15631620.13682615X-RAY DIFFRACTION100
2.4142-2.5240.18431350.13742639X-RAY DIFFRACTION100
2.524-2.65710.1521350.13732603X-RAY DIFFRACTION100
2.6571-2.82350.19331360.14232659X-RAY DIFFRACTION100
2.8235-3.04140.21261500.15242576X-RAY DIFFRACTION100
3.0414-3.34730.16291610.15362609X-RAY DIFFRACTION100
3.3473-3.83130.15881490.12852617X-RAY DIFFRACTION100
3.8313-4.82540.1331180.12592633X-RAY DIFFRACTION100
4.8254-37.57860.1935810.18482604X-RAY DIFFRACTION97
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)
10.839-0.27210.02911.237-0.38890.69910.01380.02350.04620.0394-0.0493-0.13170.01190.0745-0.00070.09340.00140.0030.1024-0.00980.123231.759710.505333.8919
20.5476-0.07140.40440.4407-0.25160.51780.0444-0.042-0.0601-0.04490.00550.0951-0.127-0.12280.00720.1008-0.0014-0.00010.1230.00790.160712.58749.629234.5348
30.05920.0246-0.14810.5563-0.02670.4041-0.2638-0.4894-0.07570.34770.1347-0.0213-0.06550.1027-0.0850.17590.02790.02830.2439-0.00430.134120.966914.282258.5803
40.6309-0.28370.20030.54820.16921.902-0.0478-0.1991-0.02350.11470.04550.0282-0.1289-0.12810.00110.18020.01210.01410.1770.00780.110920.320613.68956.4974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 206 )
3X-RAY DIFFRACTION3chain 'A' and (resid 207 through 228 )
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 334 )

+
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