[English] 日本語
Yorodumi
- PDB-5d86: Staphyloferrin B precursor biosynthetic enzyme SbnA Y152F variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d86
TitleStaphyloferrin B precursor biosynthetic enzyme SbnA Y152F variant
ComponentsProbable siderophore biosynthesis protein SbnA
KeywordsBIOSYNTHETIC PROTEIN / siderophore / iron / plp
Function / homology
Function and homology information


N-(2-amino-2-carboxyethyl)-L-glutamate synthase / transferase activity, transferring alkyl or aryl (other than methyl) groups / cysteine biosynthetic process from serine
Similarity search - Function
2,3-diaminopropionate biosynthesis protein SbnA / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / N-(2-amino-2-carboxyethyl)-L-glutamate synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsKobylarz, M.J. / Grigg, J.C. / Liu, Y. / Lee, M.S.F. / Heinrichs, D.E. / Murphy, M.E.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-102596 Canada
CitationJournal: Biochemistry / Year: 2016
Title: Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis.
Authors: Kobylarz, M.J. / Grigg, J.C. / Liu, Y. / Lee, M.S. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionAug 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable siderophore biosynthesis protein SbnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3425
Polymers35,9241
Non-polymers4184
Water6,323351
1
A: Probable siderophore biosynthesis protein SbnA
hetero molecules

A: Probable siderophore biosynthesis protein SbnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,68410
Polymers71,8482
Non-polymers8368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5110 Å2
ΔGint-34 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.360, 115.990, 45.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1279-

HOH

21A-1405-

HOH

-
Components

#1: Protein Probable siderophore biosynthesis protein SbnA


Mass: 35924.164 Da / Num. of mol.: 1 / Mutation: Y152F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Newman / Gene: sbnA, NWMN_0060 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6QDA0
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M MgCl2, 0.1 M Tris, pH 8.5, 29-33% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2014 / Details: Rh coated focusing mirror
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.5→57.995 Å / Num. all: 47701 / Num. obs: 47701 / % possible obs: 98.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.67 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Rsym value: 0.062 / Net I/av σ(I): 6.461 / Net I/σ(I): 18.6 / Num. measured all: 313063
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.584.60.2083.62849261600.1060.2085.888.9
1.58-1.686.70.1764.24393166000.0730.1769.399.3
1.68-1.7970.1255.74353762210.0510.12512.8100
1.79-1.9470.0887.54082358280.0360.08816.8100
1.94-2.1270.0718.83754753660.0290.07121.7100
2.12-2.3770.058103420749030.0230.05825100
2.37-2.746.90.05111.12980743250.0210.05127.5100
2.74-3.356.80.0579.32502937040.0240.05729.899.8
3.35-4.746.40.05410.51855928930.0230.0543299.4
4.74-38.6636.50.04412.71113117010.0190.0443199.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.5 Å35.38 Å
Translation6.5 Å35.38 Å

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.5.5phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.379 Å / FOM work R set: 0.8944 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1798 2412 5.06 %
Rwork0.1483 45232 -
obs0.1499 47644 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.05 Å2 / Biso mean: 18.13 Å2 / Biso min: 5.92 Å2
Refinement stepCycle: final / Resolution: 1.5→35.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 25 351 2832
Biso mean--21.37 29.84 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142726
X-RAY DIFFRACTIONf_angle_d1.5273722
X-RAY DIFFRACTIONf_chiral_restr0.067420
X-RAY DIFFRACTIONf_plane_restr0.01483
X-RAY DIFFRACTIONf_dihedral_angle_d14.2141041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53060.20371140.1832252236684
1.5306-1.56390.19721240.17062408253290
1.5639-1.60030.19961510.16142519267095
1.6003-1.64030.18771260.158327002826100
1.6403-1.68470.18991500.150426842834100
1.6847-1.73420.1911450.151526662811100
1.7342-1.79020.19631530.157126422795100
1.7902-1.85420.22051510.156526872838100
1.8542-1.92840.19571330.157727052838100
1.9284-2.01620.18751370.151227232860100
2.0162-2.12250.1691300.146726852815100
2.1225-2.25540.18451400.144627312871100
2.2554-2.42950.19671460.148527182864100
2.4295-2.67390.19091310.15327572888100
2.6739-3.06070.18131730.152426932866100
3.0607-3.85540.1561550.13592762291799
3.8554-35.38920.15741530.13762900305399
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)
11.9774-0.2236-0.3880.7339-0.09490.52760.09050.0612-0.0315-0.011-0.03720.0903-0.0385-0.0346-0.05340.0914-0.007-0.01870.0702-0.01260.082119.6962-8.1691-4.4832
24.76-0.04510.39314.37030.14212.8344-0.0193-0.6562-0.43830.73310.0684-0.44070.11280.13160.14150.2538-0.0146-0.04920.17720.03590.218711.6806-20.619513.1999
31.7346-0.2207-0.59450.722-0.00750.85310.0060.1048-0.194-0.073-0.0290.08340.0607-0.02850.02470.0958-0.0003-0.01470.0579-0.020.094725.9012-21.2865-7.966
40.8325-0.02780.02551.59590.07471.04780.0165-0.0599-0.07350.1482-0.0071-0.02310.05360.0765-0.00510.06540.0130.00610.07180.00890.059837.7954-17.47180.6484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:118 )A8 - 118
2X-RAY DIFFRACTION2( CHAIN A AND RESID 119:142 )A119 - 142
3X-RAY DIFFRACTION3( CHAIN A AND RESID 143:231 )A143 - 231
4X-RAY DIFFRACTION4( CHAIN A AND RESID 232:325 )A232 - 325

+
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