[English] 日本語
Yorodumi
- PDB-3rqt: 1.5 Angstrom Crystal Structure of the Complex of Ligand Binding C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rqt
Title1.5 Angstrom Crystal Structure of the Complex of Ligand Binding Component of ABC-type Import System from Staphylococcus aureus with Nickel and two Histidines
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Ligand Binding Component / ABC-type Import System / Nickel / single or di-peptides / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


nickel cation transport / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll ...Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / NICKEL (II) ION / Nickel-binding protein NikA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Kiryukhina, O. / Falugi, F. / Bottomley, M. / Bagnoli, F. / Grandi, G. ...Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Kiryukhina, O. / Falugi, F. / Bottomley, M. / Bagnoli, F. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.5 Angstrom Crystal Structure of the Complex of Ligand Binding Component of ABC-type Import System from Staphylococcus aureus with Nickel and two Histidines.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Kiryukhina, O. / Falugi, F. / Bottomley, M. / Bagnoli, F. / Grandi, G. / Anderson, W.F.
History
DepositionApr 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,77010
Polymers55,5381
Non-polymers1,2329
Water13,259736
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.941, 66.759, 115.492
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 Putative uncharacterized protein


Mass: 55538.262 Da / Num. of mol.: 1 / Fragment: Ligand Binding Component
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: SAOUHSC_00001, SAOUHSC_00201 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2G2P5

-
Non-polymers , 5 types, 745 molecules

#2: Chemical ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Protein: 7.5mG/mL, 0.5M Sodium chloride, 0.01M Tris, pH 8.3. Screen: Classics II (D8), 0.1M HEPES, pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 77770 / Num. obs: 77770 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 21.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3 / Num. unique all: 3817 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→29.91 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.124 / SU ML: 0.038
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16971 3886 5 %RANDOM
Rwork0.14117 ---
all0.14259 73346 --
obs0.14259 73346 99.83 %-
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: 15.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å2-0 Å2
2---0.11 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 73 736 4517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224272
X-RAY DIFFRACTIONr_bond_other_d0.0010.022953
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9775813
X-RAY DIFFRACTIONr_angle_other_deg0.94437330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9385548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11325.979194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.07915832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3711515
X-RAY DIFFRACTIONr_chiral_restr0.1070.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024818
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02767
X-RAY DIFFRACTIONr_mcbond_it0.9331.52605
X-RAY DIFFRACTIONr_mcbond_other0.291.51026
X-RAY DIFFRACTIONr_mcangle_it1.66824288
X-RAY DIFFRACTIONr_scbond_it2.76631667
X-RAY DIFFRACTIONr_scangle_it4.4964.51525
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 299 -
Rwork0.187 5302 -
obs-5302 99.63 %
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)
10.3546-0.1355-0.27830.58640.36140.8852-0.03040.0165-0.03710.0464-0.0171-0.00090.0331-0.02140.04750.00640.00260.00610.01650.01160.018942.178843.030813.8294
20.3238-0.1660.11071.0467-0.01040.8396-0.0413-0.02180.02580.2234-0.0098-0.1489-0.10430.1640.05110.0612-0.0201-0.04180.07230.00460.04350.267959.293229.8339
30.56410.00780.07270.95490.04990.7857-0.01310.04320.0965-0.0518-0.0129-0.0825-0.14390.07530.0260.0402-0.0186-0.00380.01280.0130.035337.752476.80514.8922
40.4349-0.0751-0.03770.73390.17330.87690.00640.01930.0237-0.0205-0.0107-0.0319-0.04580.01810.00420.0029-0.0009-0.00070.00240.00320.007934.870466.71376.227
50.64590.5360.28322.80930.36530.5816-0.01170.103-0.0010.05150.0007-0.37080.00760.28170.01090.0478-0.0117-0.02910.1550.02530.106555.894156.032123.3273
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 161
2X-RAY DIFFRACTION2A162 - 225
3X-RAY DIFFRACTION3A226 - 312
4X-RAY DIFFRACTION4A313 - 440
5X-RAY DIFFRACTION5A441 - 469

+
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