[English] 日本語
Yorodumi
- PDB-1q35: Crystal Structure of Pasteurella haemolytica Apo Ferric ion-Bindi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q35
TitleCrystal Structure of Pasteurella haemolytica Apo Ferric ion-Binding Protein A
Componentsiron binding protein FbpA
KeywordsMETAL BINDING PROTEIN / iron binding protein
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Ferric binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Fe(3+) ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesMannheimia haemolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsShouldice, S.R. / Dougan, D.R. / Skene, R.J. / Snell, G. / Scheibe, D. / Williams, P.A. / Kirby, S. / McRee, D.E. / Schryvers, A.B. / Tari, L.W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of Pasteurella haemolytica ferric ion-binding protein A reveals a novel class of bacterial iron-binding proteins
Authors: Shouldice, S.R. / Dougan, D.R. / Williams, P.A. / Skene, R.J. / Snell, G. / Scheibe, D. / Kirby, S. / Hosfield, D.J. / McRee, D.E. / Schryvers, A.B. / Tari, L.W.
History
DepositionJul 28, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 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_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: iron binding protein FbpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0494
Polymers35,8951
Non-polymers1543
Water11,025612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.159, 189.327, 45.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1166-

HOH

-
Components

#1: Protein iron binding protein FbpA / Ferric ion-Binding Protein A


Mass: 35894.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mannheimia haemolytica (bacteria) / Gene: fbpA / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q9Z4N6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: PEG 3350, magnesium formate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %PEG33501drop
20.1 Mmagnesium formate1droppH5.9
320 %PEG33501reservoir
40.2 Mmagnesium formate1reservoirpH5.9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2002
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→95.35 Å / Num. all: 123103 / Num. obs: 116923 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.2→1.24 Å / % possible all: 93.4
Reflection
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 95 Å / % possible obs: 93.4 % / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 65.7 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.6

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→35.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.53 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19511 6170 5 %RANDOM
Rwork0.17098 ---
obs0.1721 116923 93.34 %-
all-123103 --
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: 12.006 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.58 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2521 0 4 618 3143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222574
X-RAY DIFFRACTIONr_bond_other_d0.0020.022329
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.9633471
X-RAY DIFFRACTIONr_angle_other_deg0.75535465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055315
X-RAY DIFFRACTIONr_chiral_restr0.0680.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022833
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02490
X-RAY DIFFRACTIONr_nbd_refined0.2010.2521
X-RAY DIFFRACTIONr_nbd_other0.2270.22775
X-RAY DIFFRACTIONr_nbtor_other0.080.21462
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0760.2398
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.247
X-RAY DIFFRACTIONr_mcbond_it0.5781.51579
X-RAY DIFFRACTIONr_mcangle_it1.00322550
X-RAY DIFFRACTIONr_scbond_it1.3743995
X-RAY DIFFRACTIONr_scangle_it2.264.5921
X-RAY DIFFRACTIONr_rigid_bond_restr0.67622574
X-RAY DIFFRACTIONr_sphericity_free1.2772612
X-RAY DIFFRACTIONr_sphericity_bonded1.31322529
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 307
Rwork0.247 5658
Refinement
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 35.3 Å / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.094

+
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