[English] 日本語
Yorodumi
- PDB-6mjt: Azurin 122F/124W/126Re -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mjt
TitleAzurin 122F/124W/126Re
ComponentsAzurin
KeywordsELECTRON TRANSPORT / Electron Hopping
Function / homology
Function and homology information


transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding
Similarity search - Function
Azurin / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Chem-REQ / Azurin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.893 Å
AuthorsTakematsu, K. / Zalis, S. / Gray, H.B. / Vlcek, A. / Winkler, J.R. / Williamson, H. / Kaiser, J.T. / Heyda, J. / Hollas, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK019038 United States
CitationJournal: ACS Cent Sci / Year: 2019
Title: Two Tryptophans Are Better Than One in Accelerating Electron Flow through a Protein.
Authors: Takematsu, K. / Williamson, H.R. / Nikolovski, P. / Kaiser, J.T. / Sheng, Y. / Pospisil, P. / Towrie, M. / Heyda, J. / Hollas, D. / Zalis, S. / Gray, H.B. / Vlcek, A. / Winkler, J.R.
History
DepositionSep 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Azurin
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1266
Polymers28,0422
Non-polymers1,0844
Water1,67593
1
A: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5633
Polymers14,0211
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5633
Polymers14,0211
Non-polymers5422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.910, 33.970, 77.260
Angle α, β, γ (deg.)90.000, 98.550, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Azurin


Mass: 14020.887 Da / Num. of mol.: 2 / Mutation: W48F, Y72F, H83Q, Y108F, K122F, T124W, T126H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: azu, PA4922 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00282
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-REQ / (1,10 PHENANTHROLINE)-(TRI-CARBON MONOXIDE) RHENIUM (I)


Mass: 478.496 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H12N2O3Re / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.5
Details: 0.1 M NaOAc, 120 mM/150 mM Li2SO4, and 48.6% PEG 400/27.7% PEG 8000 at pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.893→38.393 Å / Num. all: 19028 / Num. obs: 19028 / % possible obs: 93.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 27.61 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.077 / Rsym value: 0.059 / Net I/av σ(I): 5.1 / Net I/σ(I): 9.6 / Num. measured all: 46285
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.89-22.50.152643526250.1210.1930.155.188.8
2-2.122.50.0997627625480.0780.1270.0996.692.3
2.12-2.262.40.0775.9596024400.0620.0990.0778.292.8
2.26-2.442.50.0679.3563022870.0520.0850.0679.394.1
2.44-2.682.40.05611513421090.0440.0720.05610.794.6
2.68-2.992.40.05311.7476919520.0420.0670.05311.895.6
2.99-3.462.40.04712.5423717470.0380.0610.04712.796.4
3.46-4.232.40.05110.5357714880.0430.0670.05113.396.9
4.23-5.992.40.0549.7277111700.0450.070.05413.497.6
5.99-38.3932.30.0865.314966620.0750.1150.0861395.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.62 Å20.99 Å
Translation4.62 Å20.99 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.21data scaling
PHASER2.5.2phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZU

1azu


Resolution: 1.893→20.985 Å / FOM work R set: 0.804 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 986 5.18 %
Rwork0.2208 18032 -
obs0.2221 19018 93.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.11 Å2 / Biso mean: 34.7 Å2 / Biso min: 10.96 Å2
Refinement stepCycle: final / Resolution: 1.893→20.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 48 93 2037
Biso mean--26.74 39.86 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081987
X-RAY DIFFRACTIONf_angle_d1.3072703
X-RAY DIFFRACTIONf_chiral_restr0.06297
X-RAY DIFFRACTIONf_plane_restr0.006346
X-RAY DIFFRACTIONf_dihedral_angle_d12.41678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8931-1.99280.26051270.24452426255388
1.9928-2.11750.28651340.2442495262992
2.1175-2.28090.26551490.22662529267892
2.2809-2.510.24471370.23292560269793
2.51-2.87250.25981450.22252617276294
2.8725-3.6160.251350.22212649278496
3.616-20.98670.22481590.20842756291596
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)
14.0234-0.03492.13612.9893-2.09275.5387-0.025-0.3148-0.9261-0.1117-0.0742-0.31371.12350.5248-1.13570.36960.21770.03320.32490.12540.4339-11.54660.089822.33
22.97290.7239-1.14662.360.91293.52510.2086-0.1939-0.420.3227-0.12-0.1337-0.0408-0.60860.09110.19270.05250.02640.38550.0650.0345-19.21678.59125.1554
37.95980.768-0.54155.16520.04255.51660.34940.2531-0.087-0.1653-0.31470.24840.0097-0.06130.05140.2644-0.0558-0.01970.40420.01750.2356-20.64397.988918.8395
40.12730.32640.25381.1015-0.53687.7450.0613-0.6374-0.31720.28210.0068-0.2116-0.04150.88430.71720.16460.05920.00670.38660.13630.0674-11.941310.138724.4991
55.34540.07240.14474.9631.31365.4514-0.1053-0.02080.7798-0.20020.00880.4216-0.8926-0.1405-0.29520.25480.1318-0.00040.18860.04390.3241-43.615.601917.6411
62.39760.5310.67462.2833-0.46624.57950.0366-0.36820.30580.2897-0.148-0.1025-0.01540.85460.03570.17220.00510.01250.2962-0.04360.0687-36.3535-1.927722.6565
71.3368-0.882.28082.0871-1.71993.9550.16240.6243-0.18460.0057-0.54970.04520.69490.5489-0.29260.4125-0.1720.13160.7665-0.18410.2796-33.6553-6.088810.6593
81.76150.83340.10791.8159-0.21244.82230.0069-0.08690.19580.0316-0.0910.3690.0749-0.50130.0160.16570.0799-0.00940.2307-0.03810.1228-43.6428-4.312319.2001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )A1 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 80 )A19 - 80
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 107 )A81 - 107
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 128 )A108 - 128
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 18 )B1 - 18
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 92 )B19 - 92
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 107 )B93 - 107
8X-RAY DIFFRACTION8chain 'B' and (resid 108 through 128 )B108 - 128

+
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